It's been a long time since the term "punk rock" could strike fear into the British establishment. The Sex Pistols' John Lydon – aka Johnny Rotten – was long ago transformed into a pantomimic national institution, and now advertises Country Life butter; it's 16 years since Tony Blair admiringly mentioned the Clash in a speech at the Brit awards. The spiky-topped punk look is as harmless a part of vernacular British style as Harris tweed; the concert nostalgia circuit is now home to any number of ageing punk groups, from the Buzzcocks to Sham 69.

The last few months, however, have brought news from abroad suggesting that in many places, punk's combination of splenetic dissent, loud guitars and outre attire can cause as much disquiet and outrage as ever. The stories concerned take in Indonesia, Burma, Iraq and Russia – and most highlight one big difference between the hoo-hah kicked up by punk in the US and Britain of the late 70s, and the reactions it now stirs thousands of miles from its places of birth. Back then, being a punk rocker might invite occasional attacks in the street, a ban on your records, and the odd difficulty finding somewhere to play. Now, if you pursue a love of punk in the wrong political circumstances, you may well experience oppression at its most brutal: torture, imprisonment, what one regime calls "moral rehabilitation" and even death.

First, then, to Iraq, and news that will surely warm the heart of anyone who still believes the US and Britain attacked that country to introduce it to the wonders of democracy and tolerance. Last weekend, Reuters reported that at least 14 young people had recently been stoned to death in Baghdad, thanks to "a campaign by Shi-ite militants against youths wearing Western-style 'emo' clothes and haircuts".

For the uninitiated, "emo" is short for "emotional hardcore", and refers to a music and dress-code traceable to a variety of punk invented in Washington DC in the mid-1980s, lately smoothed out and rendered massively lucrative by such teenage favourites as Fall Out Boy, Panic! At the Disco and Paramore. In February, the Iraqi interior ministry said it equated "the 'emo' phenomenon" with satanism, and warned of young people who "wear tight clothes that bear paintings of skulls" and favour "rings in their noses and tongues as well as other weird appearances". The same ministry has since denied that emo had anything to do with the killings, claiming that "no murder case has been recorded with the interior ministry on so called 'emo' grounds. All cases of murder recorded were for revenge, social and common criminal reasons."

One thing is definitely true: figures for emo-related killings are blurring into those for homophobic murders (put at up to 58 in the last six weeks alone), reflecting a widespread perception in Iraq that emo is a byword not just for devil-worship, but homosexuality. A leaflet distributed in east Baghdad gave any local emo fans four days to "leave this filthy work", under pain of "the punishment of God … at the hand of the Mujahideen". At least two lists of intended victims have been posted online, and tattoo parlours in the city have reported terrified young people asking for their punk-esque body-art to be removed.

In Moscow, a court ruling on Wednesday marked the latest chapter in the story of an all-female band called Pussy Riot, two of whom were arrested last month after they illicitly took over the pulpit in a Moscow church, and attempted to recite a "punk prayer" written in opposition to Vladimir Putin. Pussy Riot's music is scratchy, unhinged stuff that takes its lead from a fleeting genre known as riot grrrl – once again traceable, at least in part, to Washington DC, and brought to fruition nearly 20 years ago by such groups as Bikini Kill, and a British band called Huggy Bear. Their music was clearly derived from punk's basic idea, but took its lead from such feminist groups as the Slits and the Au Pairs rather than the Clash and the Pistols: apart from anything else, the controversy around Pussy Riot has at least served as a reminder of this overlooked strand of punk history.

"We somehow developed what [those groups] did in the 1990s, although in an absolutely different context and with an exaggerated political stance," one band member called Garadzha Matveyeva has explained, "which leads to all of our performances being illegal – we'll never give a gig in a club or in any special musical space. That's an important principle for us." The band, who always perform in identity-concealing balaclavas, has a free-floating membership that can number up to 15 people – it amounts to "a pulsating and growing body", as Matveyeva sees it. This week, the two members who were arrested had their detention extended by six weeks: Nadezhda Tolokonnikova and Mariya Alekhina are both young mothers who are reported to be on hunger strike, and face charges of "hooliganism" that could lead to prison sentences of seven years. One of Russia's leading Muslim clerics, Muhammedgali Khuzin, this week suggested they should be sentenced to "removing garbage from the streets of Moscow": a way, he says, of "clearing your head of trash".

In Burma, the country's punk rock milieu has been fomenting since around 2007, when musicians came together in brazen opposition to the country's ruling junta. Its most notable representatives are two bands, No U Turn, and the Rebel Riot, both of whom favour the mohicans-and-studs look de rigeur on the Kings Road circa 1980. The Rebel Riot are led by 24-year-old Kyaw Kyaw, who works in a Rangoon textile factory for around £40 a month. His band and their fans seem to be tolerated by the authorities, but are regularly harassed by police; there are also widespread suspicions that punk audiences are usually smattered with undercover police.

The Rebel Riot's lyrics need no explanation: "No fear! No indecision!/ Rage against the system of the oppressors!"; "We are poor, hungry and have no chance/ Human rights don't apply to us/We are victims, victims, victims." According to a recent article in the German magazine Der Spiegel, many of their gigs are organised by a local punk impresario called Ko Nyan: his founding place in Burmese punk culture was sparked when he found a magazine featuring the Sex Pistols in a bin behind Rangoon's British embassy.

What all these stories highlight is the ongoing vitality of a musical form that, in its homelands, has tended to fall into self-parody. To jaded western eyes, many of the groups and fans appear to be straight out of central casting, and the music can sound hopelessly derivative, rather clumsy, and in thrall to influences whose cultural charge faded three decades ago. Some of the musicians' chosen western reference points are almost comically unlikely. But that is our problem, not theirs: to paraphrase Johnny Rotten, they mean it, man.

In the altogether more placid environs of Copenhagen, an organisation called Freemuse – which claims to be "the world's leading organisation advocating freedom of expression for musicians" – attempts to keep tabs on the persecution of musicians across the planet, and its programme director, Ole Reitov, is all too aware of the fact that punks currently seem to be disproportionately in the line of repressive fire.

"You hear a lot about the clash of civilizations," he tells me, "but often, these things, they reflect a clash within civilizations. You're seeing the same symptoms in all kinds of countries: it's a matter of what you do if you feel you're powerless. You can only be extreme, relative to so-called normality."

He thinks all this will only increase given two parallel developments: the rise of religious fundamentalism, and the increase in networked communications, which means that every aspect of a subculture can be globally spread at speed. "Think back 50 years," he says. "People didn't necessarily know what the Shadows or the Beatles looked like. These days, you immediately know. Someone in Ulan Bator immediately knows the body language that comes with rap music; in Iraq, the young people who've been killed knew how to dress a certain way."

In December last year, a punk gig took place in Aceh, Indonesia, the "special province" of the country that has its own police force pledged to maintain sharia law. Supposedly because the event's organisers had forged official documents to gain the requisite permit, 64 of its attendees – who had travelled from all over the country – were arrested, and taken to a nearby detention centre, before being transported to a "remedial school" 37 miles away. There, their mohican hairstyles were forcibly removed because they were deemed "insulting to Islamic traditions". According to a police spokesman, the group was held there to "undergo a re-education, so their morals will match those of other Acehnese people". Demonstrations followed not just in Indonesia, but in London and San Francisco.

The story was the latest twist in the 20-year history of Indonesian punk, explained down a phone-line from Jakarta by 30-year-old Fathun Karib, a member of a punk-metal group called Cryptical Death, and author of a doctoral thesis on the subject. He puts the events in Aceh down to local politicians running for elections. "They want to build up an image," he says. "They use sending the punks to moral rehab as a pretext, to prove they're doing a good job. In the perspective of people in Aceh, punk is a social problem. So it's really a game." He goes on: "But now, the punks have access to international networks, so the issue became bigger than the local politicians expected."

There are, he tells me, two kinds of punk in Indonesia. "One is what we think of as a poser: they adopt punk fashions." This group, he says, tend to be "street kids" who fall into begging and petty crime, and thereby provoke the authorities. "The other punks are part of a community that has developed since the late 80s – a moral, ideological type of community," he says. "They're totally different. But the government and society thinks that if you have a Mohawk and boots, you are a punk, and all punks are the same." The kids arrested in Aceh, he thinks, are likely to be the genuine article, because they were arrested at a gig, a reasonably sure sign of true believers.

The first wave of Indonesian punk stretched from 1990 to 1995, and saw the arrival of groups called Submission, Antiseptic and the elegantly named Dickhead. It was sparked by records by such British punk groups as the Sex Pistols and the Exploited, a Scottish band whose take on punk could charitably be construed as somewhat reductive (older readers may remember their debut album, Punks [sic] Not Dead, and their only performance on Top of the Pops in 1981, much discussed in British schoolyards the following day).

A second Indonesian phase began in 1996, inspired by a US punk fanzine and record label called Profane Existence, and the British band Crass, who shared an essentially anarchist ideology. This development played into a sea change in Indonesian public opinion, as opposition to the Suharto regime – which fell in 1998 – hardened. With the regime on its last legs, says Karib, punks tended to be left alone. "We continued to play, without much attention from the authorities," he says. "They were focused on the student movement, not music."

A third phase, he says, saw the punk scene become "more international" – a development marked by a famous occasion when the Exploited played in Jakarta in 2006. And from then until now, punk rock has rooted itself across Indonesia. "There are thousands of bands now," says Karib. "You can find punks around the country. They're in Sumatra, Jakarta, Bali … everywhere." Given punk's arrival in ultra-conservative Aceh, he suspects that events of last year will be replayed, and that the reaction will once again be global.

Towards the end of our conversation, I ask him the inevitable question: what appeals to him about a music and subculture that will soon be 40 years old? His answer is spoken with the same passion you would have found in London during the hot punk summer of 1976. "It's simply an expression of freedom," he says. "It has those do-it-yourself values. And it's always opposed to the dominant culture. That's why people like it."