The small gay community in conservative, Muslim-majority Indonesia is facing a sudden and unexpected backlash, with ministers and religious leaders denouncing homosexuality, LGBT websites blocked and emboldened hardliners launching anti-gay raids.

When a minister criticised counselling services for gay students at a university last month, it triggered a heated media debate and was the start of what activists say has been a sustained assault on gay rights.

Hardline Defence Minister Ryamizard Ryacudu this week labelled the influence of the gay community "a threat" and said fighting it was akin to "a kind of modern warfare".

"It's dangerous as we can't see who our foes are, but out of the blue everyone is brainwashed," he was cited as saying by news website Tempo.

The government has shut down a slew of websites, ordered TV programs depicting gay lives off the air and demanded all instant messaging apps remove same-sex emoticons -- like men holding hands and the symbolic rainbow flag -- or face a ban.

Indonesia's top Islamic clerical body has revived a push for gay sex to be criminalised, saying it is not only "deviant" but against the country's founding principles, and lawmakers are reportedly considering drafting an anti-homosexuality bill.

Homosexuality is generally taboo in the world's most populous Muslim-majority nation and gay people have in the past suffered verbal and physical attacks.

However it is legal in most of the country, with a notable exception being ultraconservative Aceh province, and homosexuals have mostly been able to quietly get on with their lives.

It is unclear why the recent furore has gained such momentum, but it follows a push by religious leaders and conservative politicians to bolster public morality in Indonesia, with crackdowns on prostitution and the availability of drugs and alcohol.

Activists also say that gains made abroad for LGBT rights, particularly the legalisation of same-sex marriage across the entire United States in June, have heightened scrutiny of Indonesia's gay community and fanned homophobia.

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Much of the concern from senior political figures has revolved around a sense that the LGBT (lesbian, gay, bisexual and transgender) community is seeking to push for changes viewed as contrary to Indonesian culture, like same-sex marriage.

"What's forbidden is (groups) saying 'Hey you, let's be lesbian and gay.' That's wrong," said Vice President Jusuf Kalla, who has requested the United Nations Development Fund not finance LGBT programs in Indonesia.

- 'It's become dangerous' -

Those working with the gay community say there has been a corresponding spike in harassment, stalking and online abuse, with many fearing radical groups railing against a so-called "LGBT emergency" could become violent.

Radical group the Islamic Defenders Front has stormed boarding houses in the city of Bandung hunting for same-sex couples, while in Yogyakarta radicals massed outside an Islamic school famous for accepting transgender students.

Hardliners have been putting up signs denouncing homosexuality and scuffles broke out this week as police stopped a rally by supporters of the gay community from going ahead in Yogyakarta, several hundred kilometres east of Jakarta.

"It's getting worse and worse. It's become dangerous for us," Ryan Korbarri, general secretary of gay outreach group Arus Pelangi, told AFP.

Staff at the organisation have started travelling in pairs and taking different routes home, while another Jakarta-based group Suara Kita shut its distinctive rainbow gate for the first time ever, biding time until the heat dies down.

The unusual wave of anti-gay rhetoric -- particularly from senior government officials -- has shocked rights activists at home and abroad, with President Joko Widodo being urged to uphold Indonesia's national motto "unity in diversity".

"President Jokowi should urgently condemn anti-LGBT remarks by officials before such rhetoric opens the door to more abuses," said New York-based Human Rights Watch, referring to the president by his nickname.

Despite his silence so far, many still have faith in Widodo, whose past promises to address human rights abuses and champion minority groups have earned him the strong backing of almost all LGBT people in Indonesia, said Teguh Iman from Suara Kita.

"I hope Jokowi will say something about this, and hold us up as equal citizens," he said.