You lose count of the number of times you hear documentaries trashed. The argument is as old as the documentary, and it goes like this. Docs manipulate reality, over-relying on effects such as music. They aren't really journalistic at all. Maybe one should think of them as drama without actors, cheaply made and with few pretensions to seriousness. Shamelessly, they pander to our worst voyeuristic impulses. Under the guise of telling the truth, docs entertain us with lies.

It would be more accurate to say that documentaries are among the most valuable, neglected cultural forms of our time. They aren't all good, to be sure, but the best are unusual, persuasive, seductive. And their success has something to do with the way they are taken for granted, casually watched. Few old things have flourished in the cultural chaos of this century, but docs have steadily consolidated their hold on a small portion of the contemporary consciousness. Film stars want to make or sponsor them. Sometimes, if you squint hard enough, they really do seem like the new rock'n'roll.

Criticism of documentaries comes in waves. A few years ago, spotting fakery in docs was in vogue, though it seemed that most docs were scrupulously, often tediously, unfaked. Now the critics have latched on to the vulgarity of peak-time docs. Channel 4 has been slated for My Big Fat Gypsy Wedding. Was the series set up in some respects? Did it end by stereotyping Romanies under the guise of complaining about their stereotyping? The critics also complained about the superficiality of Niall Ferguson, whose Channel 4 series, Civilization, runs us through the west and its discontents.

But the most acrimonious debate surrounded the attempts of physicist, and heartthrob, Professor Brian Cox to explain the secrets of the universe in Wonders of the Universe. Master of the Queen's Music Sir Peter Maxwell Davies complained about the use of "Muzak" in the BBC2 series. "Viewers have not tuned in to listen to a musical performance," he declared.

I didn't much like Ferguson's leather jacket. I also think he should try to convey to audiences that he cares about what he's saying – something he does in his lectures, but mysteriously fails to do on television. And, yes, I did think that Channel 4's wedding series contained a few too many Gypsy flounces. But I was seduced by Cox's meditations. He made me recall hours spent watching a black-and-white box as a teenager. I don't know much about the universe, beyond the piece I occupy, but now I wanted to know more. And I'm sure that many of its five million viewers felt the same.

Many criticisms of documentaries contain an unpleasantly snobbish undertone. Why object to shows like The Secret Millionaire, which do supply a vision of real life even as they follow a formula?

"Documentary," says the dictionary. "Noun. Based on or recreating an actual event, era, life story, that purports to be factually accurate and contains no fictional elements." This is useful, but a trifle over-cautious. Why shouldn't non-fiction contain elements of fiction? And why should something only "purport" to be factually accurate? It reeks of the old charges that docs are unreliable because they are filmed. When you describe anything, it is altered. The act of seeing modifies what is seen. Most people who watch docs understand this.

I'm a professional watcher of documentaries, but I'm also an addict. Within the dullest doc, I usually find something interesting. In an age when television drama is predictable, docs offer us real, often alien voices. They also fill some of the void left by the emptiness of much television reporting.

No body of theory exists to legitimise docs and I'm grateful for this. They have come to subsist at a crossroads of contemporary culture, somewhere between journalism, film narrative and television entertainment. They appear to thrive on contradictions, between the stubborn reality they purport to capture and their necessarily limited means, between the impositions of storytelling and the desire to interpret or analyse. They aren't fictional, ever, but they can seem in their attractiveness more real than reality.

In recent years, docs have often performed well in cinemas. It has become customary at chic festivals to hear people say how much more interesting they are than the narrative fictions on offer. I don't think docs can or should try to stand in for Hollywood fare. They do something different. A film like Man on Wire was a way of approaching the 9/11 attacks at an angle, elegiacally, getting us to imagine what the twin towers meant by seeing someone walk between them.

This year's Oscar winner, Inside Job, an unflinching account of the venal goings-on that led to the 2009 Wall Street crash, has been justly praised. Its director Charles Ferguson's brilliant, unforgiving interviews have become the way we remember the crash. When he thanked the Oscar audience for giving him the opportunity to say that not one individual has been found guilty of fraud in relation to the crash, I felt it was a vindication of the capability of good documentaries. Film can speak truth to the powerful. And people will listen.

But I worry about the future of docs. Of course the supply of docu-soaps won't be allowed to dry up. I imagine Chinese versions of Niall Ferguson showing up to tell us where we screwed up. However, budgets are falling as television strives to focus on whatever is popular. It is getting harder to sustain the rarer fowl in the documentary menagerie.

I recently talked to television critic AA Gill about this. He suggested that anyone wanting to make a film could now go and do it, so simple had the technology become. One might only make one film in life, but it could be a good one – and that would ensure the future of documentaries. People do make brilliant first films, but rarely. It takes time to become really good. The best docs are provisional. They seem to come from beyond the perimeters of the world, which accounts both for their freshness, and the relative poverty of those who make them.

One such film, shown this week on BBC4, is Marathon Boy, which tells the story of Budhia, an Indian boy who ran astonishing distances. He was adopted by his trainer and found himself at the centre of a controversy involving politicians, social workers and journalists. Is stardom a way out of poverty? Who has the right to define abuse? For film-maker Gemma Atwal, born in India and adopted by an English couple, such questions are far from remote. Without giving answers, the film brilliantly explores Budhia's fate. It's easy to talk about the effects of poverty, but in this film you can see them.

Will these documentaries – low budget, clever, appealing to small, passionate audiences – be adequately funded in the squeeze on television budgets? I'm starting to worry. I'd like to know how their independent spirit can be conserved and nurtured.

In the meantime, let me suggest a way in which we might start to think about documentaries. Of the current manifestations of contemporary culture, which would you choose to preserve? Thought of as an app, documentaries wouldn't make it. They have no real cultural recognition. They will always be seen as part of something else – film, television, journalism, even real life. But you would miss them if they went. My hunch is that you would miss them very much.

Nick Fraser is series editor of Storyville on BBC4