"Half of Samara knows you're here," says a leading fixer in the city's property business. He adds, with slightly theatrical menace, that unnamed people are keeping tabs on my movements, and during my stay a mysterious yoga teacher and ex-jailbird called Bizon – bearded, like a cut-price Rasputin – keeps appearing and disappearing. It's not so very scary, except that this is an area where property politics is a serious business. In 2004 the chief architect in the next-door city of Togliatti was murdered, for getting in the way of the wrong people.

What is at stake is a city whose fragile beauty could, like the proverbial tree falling in the woods, soundlessly disappear. It is an extreme example of what is happening all over Russia, where historic cities are almost defenceless against development, corruption and obliging local governments. Most were hidden from view in Soviet times, but their heritage is the equal of better known cities in western Europe. The recent removal of Moscow's Mayor Luzhkov, under whom the capital's built fabric was ravaged, gives a glimmer of hope: Luzhkov's Moscow set a pattern which provincial cities followed and, if you were seriously optimistic, you might think that this pattern will now change.

The centre of Samara is a varied but harmonious ensemble made up of thousands of decorated wooden houses, of a unique and graceful variant of art nouveau and of brave and hopeful buildings from the early revolutionary years. The setting is magnificent, above a broad sweep in the Volga, one of the great rivers of the world. Much of it has gone already, burnt, bulldozed, blighted or left to rot. Pustular new towers erupt from the waterfront and skyline. Almost everything that's left could go too, thanks to local government that could most charitably be described as supine. With its wooden streets and waterside setting Samara could – still, just – be a Russian San Francisco. But it is heading rapidly towards being an assembly of developers' junk, like very many cities in very many parts of the world.

You probably haven't heard of Samara, even if it is the sixth largest city in Russia, and architecturally unique. This spot, more than 500 miles east and south from Moscow, doesn't impinge much on western European minds. Great battles were not fought there, although in 1941 the Russian government evacuated to Samara, which was called Kuybyshev in Soviet times. After the war it became a centre of the rocket-building industry, and a closed city. Such foreign visitors as were permitted were transported in vehicles with curtained windows. A cluster of masts still stands on the outskirts, erected to jam transmissions from the BBC World Service and Voice of America. Samara hasn't fully recovered the habit of reaching out to the world.

Samara's greatest period, about a century ago, was cut short by war and revolution, giving little time for its identity to be shaped by art and literature. For a few decades people compared its growth rate to Chicago's, and its newly wealthy merchants built lavish houses designed with bravura and skill. These include the Kurlina House, which cost three or four times the going rate for luxury houses, and the Dacha with Elephants, a landmark famous for its sculptures of the beasts, built for the artist and entrepreneur Konstantin Golovkin. He, like others of his kind, only got to enjoy his property for a few years before the communist government forced it into collective ownership.

The communists exercised a certain brutality on the city's fabric, demolishing dozens of churches and monasteries, but they also left further monuments that inspire ambivalent admiration. Constructivism, the style of the 1920s and early 30s, is exhilarating for its daring and freedom, but you catch your breath when you find that a graceful and optimistic construction is called the Dzerzhinsky Club, after the founder of the KGB. Under Stalin the official style became more conservative, but its works still have a dignity that transcends the sinister politics behind them. These include the Krasnaya Glinka Sanatorium, built for the benefit of senior party members on a high bluff upriver, now a mesmerising ruin where a Fellini would love to film.

These works – millionaires' mansions and workers' clubs – sit among courtyarded wooden houses that are the stuff of Samara. Some are richly decorated and some are more simple, but collectively they create the special atmosphere particular to timber construction. It is a kind of peacefulness to do with the fact that the building's origins, as trees, are more evident than in masonry construction, as are the signs of the handiwork done to them. A street of wooden buildings seems more intimate and warm than a stone one; it is rare to find a city the size of Samara's old town made of them. Arranged according to a grid plan laid out under Catherine the Great, they are flexible and adaptable within an overall order, while the courtyards engendered communities of the families living round them. The same flexibility means they can respond to modern needs – the Samara-born architect Vitaly Stadnikov has demonstrated how the densities of the new tower blocks could equally be achieved by renovating the courtyards.

Wooden houses are primal – you can imagine building them yourself – but they are also, with their warpings and twistings and palpable proneness to rot and fire, vulnerable. They look as if they can vanish as easily as they came. Which is exactly what is happening in Samara, where thousands of historic houses have already disappeared. Last year the conservation groups Save and Moscow Architecture Preservation Society (maps-moscow.com) published a report on the city which said that "the devastating pace of destruction and decay" threatens "to remove its identity from the face of the earth". Architecture in Samara, says the report, "has been reduced to the role of handmaiden to semi-criminal business circles."

The ministry of culture for the Samara region agrees, saying: "The lack of acknowledged value of architectural and town planning heritage, including the economic aspect, and in the end, simply a lack of responsibility, brings damage to cultural heritage no less than enemy bombing." The regional government pins the blame on the next tier down, the city government: "Samara's architectural heritage does not have a reasonable and caring boss… as long as there is no deep-rooted change in the consciousness of the city's inhabitants and primarily in the consciousness of the municipal administrators, the threat to Samara's cultural heritage will remain."

Ownership of blocks, collectivised in communist times, is now often unclear, leaving residents insecure. Sometimes developers can acquire the right to rebuild an entire block, for a few tens of thousands of dollars. Sometimes site clearance is accelerated with arson, and burnt-out wrecks dot the city. Many are owned by the local government, and are often the worst maintained.

In place of the intricate tissue of courtyards, lumpen gimcrack multi-storey blocks appear, without the slightest pretence of assimilation, and fronted by arid, gated aprons of tarmac. Buildings other than the wooden houses don't fare much better. The art nouveau works are also crumbling and subject to fires, their carvings disintegrating and disappearing. On constructivist buildings clunky plastic-framed windows have replaced the elegant originals. A very few historic buildings have been subject to something called "restoration", whereby a glutinous simulacrum of the original facade is created, behind which you find standard suspended ceilings and fluorescent lights.

In other places you might look to local government to provide protection for the historic fabric, but here it appears to be destruction's main accomplice. In 2009 the city government cut the list of 2,000 buildings thought worthy of protection by several hundred. The list is in any case secret, so the public don't know what is protected and what is not.

It's not encouraging that, following the election of the current mayor Viktor Tarkhanov in 2006, the city appointed several associates of the company SOK, which since the mid-90s has aggressively taken over several businesses, to positions of influence. According to Vasili Sergeev, on the website kompromat.ru, "several members of the group specialised in murdering for money, drug trafficking, and extortion". Sergeev reports that the deputy head of property, the head of the department of architecture, the head of the department of transport and four others had SOK links. Such people are unlikely to let some old wooden houses get in the way of their plans.

Problems are exacerbated by the division of power between local city government, and regional government, which is appointed from Moscow. Each has responsibilities for historic buildings and planning, and their frequent inability to agree creates power vacuums which developers can exploit.

I visit Aliya Chebutaryova, main state inspector of the Administration of Russian Cultural Protection Committee in the Volga Region. She is young, seems serious about her work, and loyally refuses to criticise her bosses, but her many-worded job title disguises the fact that she runs a department of one – herself – which until 2008 had seven to 10 staff.

On behalf of the regional government, she must, alone, look after the 57 historic buildings in the Samara region (of which 50 are in the city itself) that are regionally listed – that is, on the middle tier below federal monuments and above those "protected" by the city. She must inspect their condition, and report on them, after which the ministry of culture may or may not impose a list of obligations on – if they can be found – the building's owners. If the owners fail to comply the ministry can go to court and have the building given to someone else who will take better care of it. At least they can do this in theory. In practice, despite the awful condition of many such buildings, such a seizure has never happened in Samara. Part of the problem is that owners willing and able to look after them responsibly can't be found.

Chebutaryova has, in other words, an almost impossible job, which does not speak volumes for the regional government's commitment to its heritage, but the main responsibility for Samara's fabric lies with the city government. So I seek an interview with the deputy mayor Sergei Arsentyev, the politician with most responsibility for planning. He has a reputation as a hard man, yet he seems afraid of meeting the man from the Observer: my meeting with him is twice rescheduled, then cancelled. He has, I am told, an urgent call to look at a hole in a road, of which Samara has many. A little while later Arsentyev abruptly leaves his job.

So my threatening property development fixer remains the main voice of the planning and development community in Samara. "Corruption in Samara is nothing," he tells me, offering an alternative view to almost every other Samaran I meet. "Corruption only appears where there is big money, and there is no big money in Samara." The problem rather is with Russia's federal government, which should give tax breaks to owners of historic buildings, so they can afford their upkeep. He might have a point, but the prospect of slow-moving Moscow introducing this any time soon, in hard times, is almost zero. He knows this, and it's a convenient way of deflecting the issue away from the here and now.

He also gives many reasons why people will always prefer to live in new buildings. "What car do you drive? Do you like Skodas? How can you make people like Skodas if they don't want to? You can't force people to wear a pair of shoes they don't like unless you threaten to shoot them. Old buildings smell," he adds. I live in an old building and it doesn't smell, I tell him, but he doesn't want to know.

Now the struggle over Samara's heritage has crystallised round a single building, the canteen built in 1932 for the Maslennikov factory. This was idealistic in intention and design, the idea being that this culinary facility would liberate women from domestic chores. It was designed, unusually for the time, by a woman, EM Maximova. Its plan takes the form, when seen from above, of a hammer and sickle, and it was internationally famous in its day.

Its original delicacy and airiness was modified in Stalin's time and is now badly battered, but it remains underneath an extraordinary and restorable building, which would certainly be listed in Britain. For 17 years the federal ministry of culture has pressed the regional government to protect it, and is now threatening court proceedings. Despite their fine words about the importance of "cultural heritage", the regional government's minister of culture, Olga Rybakova, returns without reply letters written to her urging action, even from high levels. Meanwhile the city government has approved a somewhat ill-defined plan, proposed by SOK, to build 82,000 square metres of commercial space on the site.

The architect Vitaly Stadnikov and others have launched a campaign to save it, including protests, mass bike rides (veloden.ru/) and a techno song. It seems quixotic, but they say they are amazed by the support they have received, especially from the young. "Young people see the city is turning into a rubbish dump," says one protestor, "and losing its variety with so many monotonous buildings."

Samara now is where San Francisco was in the 1960s, when its wooden houses were threatened with comprehensive development, or Covent Garden in the 1970s. In both cases local activists defeated the developers, and eventually demonstrated the economic value of old places. The buildings that had been scheduled for demolition became desirable and valuable.

There is a chance that this could happen in Samara, but the odds against are stacked higher. Shootings were not part of the Covent Garden debate. My fixer friend, meanwhile, is baffled by the support for the old canteen building, and asserts that it must have been financed by commercial enemies of SOK. Then the menace returns. "They should shut up about the canteen," he says. "Anything could happen to it. It could burn down."