NEW DELHI: It takes courage to accuse a powerful politician ─ a man who would go on to become India's prime minister ─ of encouraging riots against a minority.

Police officer Sanjiv Bhatt did just that. And he says he is paying the price for it.

Read: Indian widow fights Modi in "final" court battle over deadly Gujrat riots

Bhatt was arrested months after he filed an affidavit in the Supreme Court in 2011, alleging that Narendra Modi incited anti-Muslim violence that killed more than 1,000 people in the western state of Gujarat.

At the time, Modi was the chief minister of the state, and Bhatt was an officer of the police intelligence.

Then, earlier this year, Bhatt was fired after 27 years on the job for taking more leave than he was allowed.

His dismissal comes amid the stiffest crackdown in decades on critics and activist and aid groups perceived to be undermining India's image and interests.

Since Modi took office last year, more than 9,000 humanitarian and human rights groups have lost their registration to receive foreign funding, effectively shutting many down, and dozens of activists have been threatened with arrest.

"Governments in general don't like criticism," said Teesta Setalvad, an activist fighting for the survivors and victims of the Gujarat riots who has been repeatedly harassed by authorities. "This particular government, from all its actions it is clear, is especially intolerant of any criticism."

Setalvad, a vocal Modi critic, had her home and office raided in July by investigators searching for evidence of embezzlement, and one prosecutor has called for her arrest, describing her as a threat to national security.

The government denies efforts to silence dissent.

Nalin Kohli, a spokesman for the ruling Bharatiya Janata Party, says that cases such as Bhatt's are for the courts to decide. But the government has made clear it views aid organisations, particularly foreign ones, with deep suspicion.

Authorities started imposing restrictions after a government intelligence report last year said that local activists were working on the orders of foreign powers to undermine India's economic growth.

The report said India lost up to 3 per cent of GDP when groups like Greenpeace rallied communities against polluting industries.

Greenpeace India said its bank account has been frozen for months, and in January one of its activists was barred from boarding a flight to London, where she was to tell British lawmakers about a coal mining project in India, after she was told she was on a list of people not allowed to leave the country.

Finance Minister Arun Jaitley said the government's restrictions on humanitarian groups and their "donor-driven activism" were merely to hold them accountable.

That has had a chilling effect.

Three humanitarian groups interviewed by The Associated Press refused to speak about the crackdown on the record for fear of government reprisals. All three said their projects, ranging from health to women's empowerment, are being closely scrutinised by authorities and negative publicity could jeopardise them.

"Any kind of organised or institutional protest or criticism is clearly under greater threat under this government. There's no doubt about that," said Mukul Kesavan, a historian at New Delhi's Jamia Millia Islamia University.

Modi, however, enjoys wide support among Indians. He led his party's landslide victory in general elections in 2014, and has an almost cult-like status in the country.

Most of his supporters do not see the crackdown against the critics as a problem, and many are supportive.

Part of Modi's persona, and that of his party, is built around Hindu nationalism, which appeals to fundamentalists and radicals.

Modi's election encouraged and gave voice to such groups, who until then had remained on the fringes of politics in the largely secular country. Today, few people among his supporters are willing to believe that Modi was complicit in the 2002 riots, citing the fact that no court has found him culpable.

Bhatt, however, says he has no doubts about Modi's involvement.

2002 riots

Bhatt was an officer with the intelligence bureau in the western state of Gujarat in 2002 when a train filled with Hindu pilgrims was attacked by a Muslim mob in a small town.

A fire erupted under mysterious circumstances and 60 Hindus burned to death. In retaliation, Muslims were attacked across the state, and more than 1,100 people ─ mostly Muslims ─ were killed in ensuing riots.

As investigations into the violence dragged on for years, Bhatt felt compelled in 2011 to go to India's Supreme Court. He submitted a sworn affidavit saying that shortly after the train fire, Modi told a meeting of top police officers and administrators that Muslims needed to be "taught a lesson" and the state's Hindus needed to be allowed to "vent out their anger".

Modi has never directly addressed Bhatt's claims and no evidence directly links him to the violence. He has dismissed all allegations that he or his government had any role in the riots, and he has not been charged with any crime.

Bhatt, a Hindu, says the violence changed "everything I stood for until then".

"I've seen riots before. Two sides fighting each other," he said. "2002 was different. The police and the state connived in the destruction of Muslim life and property."

Modi's supporters reject Bhatt's claims, saying that it's just his word against the prime minister's. They deride him as a front for the political opposition, noting his wife once ran for election representing the opposition Congress party.

Five months after he went to the Supreme Court, Bhatt was arrested for fabricating evidence.

His arrest came after a policeman who assisted Bhatt recanted testimony that Bhatt had been present at the 2002 meeting of government officials. Bhatt, who was freed on bail 17 days later, says the policeman recanted under government pressure. The case against him has been put on hold by the Supreme Court.

Bhatt acknowledges that he did take extended leaves of absence to appear before government commissions investigating the riots and his allegations and for court appearances, but says that dismissing him on those grounds is politics.

He says the threats and firing haven't surprised him. "That's just the kind of person he is," he said, referring to Modi.

Taking on the state

Setalvad's organisation, Citizens for Peace and Justice, was formed after the Gujarat riots to help families of victims navigate India's daunting and glacial justice system. She and her colleagues felt a sense of fear as soon as they got involved in the riot cases, she said.

"We were very clearly saying that Modi was guilty of administrative lapses if not criminal charges," she said. "But then we were taking on one state government."

She says that witnessing Modi's rise to national power has been "Kafkaesque and quite bizarre".

Since taking on the riot-related cases, Setalvad and her organization have been also been accused of receiving funds illegally, breaking foreign exchange laws and coaching witnesses. Setalvad has denied all charges and hasn't been formally charged with any wrongdoing.

In July, the Central Bureau of Investigation raided her home and office in Mumbai looking for evidence that Setalvad and her husband siphoned millions of rupees from her organisation for big salaries and splurges on luxury items.

Soon afterward, a government prosecutor asked that she be arrested to investigate whether her organisation misused funds it got from the Ford Foundation. She was granted anticipatory bail by a court and has managed to avoid jail.

The Ford Foundation, one the United States' largest philanthropies, has given Setalvad's organisation hundreds of thousands of dollars in funding since 2004. In April, India's Home Ministry ordered that the foundation get government clearance before giving funds to Indian partners.

The restriction, rare in India, prompted the US State Department and American ambassador to express concern publicly.

Kohli, the BJP spokesman, denied that the government is targeting Setalvad, saying that if she has nothing to hide, then she has nothing to fear.

Setalvad said the crackdown on activists comes at a time when crucial cases from the 2002 riots are about to come before the Supreme Court. "The state is making every attempt to subvert the process of justice," she said.

Kesavan, the historian at Jamia Millia Islamia University, described the steps authorities have taken against Setalvad's organization as "incredibly vindictive".

"What we're seeing here", he said, "is an attempt to push the envelope on what the state considers the boundaries of free speech."