The US foiling of an alleged plot to assassinate a prominent Sikh separatist on American soil has shone a harsh light on India’s covert operations abroad and created a potential obstacle to the deepening alignment between the world’s two largest democracies.

The case of Gurpatwant Singh Pannun, along with the June murder of Hardeep Singh Nijjar in a Vancouver suburb, has triggered alarm about a possible pattern of malign behaviour by India, as Prime Minister Narendra Modi projects a more muscular role on the world stage.

The Financial Times reported on Wednesday that US federal prosecutors had filed a sealed indictment in a New York district court against at least one alleged perpetrator of a plot to kill Pannun, a US and Canadian citizen and advocate of an independent Sikh state of “Khalistan”.

US President Joe Biden raised the alleged plot against Pannun in a discussion with Modi during the G20 summit in New Delhi in September, the FT reported.

Analysts said the White House’s response on Wednesday that it was treating the Pannun case with the “utmost seriousness” would make the incident hard for India to dismiss.

The allegations come at a delicate moment for Washington and its allies — including the Five Eyes intelligence-sharing network that groups the US, Canada, Australia, New Zealand and the UK — which are courting India as a rising military, trade and technological counterweight to China.

Canada’s Prime Minister Justin Trudeau said in September that the country’s security services were investigating “credible allegations” linking New Delhi to Nijjar’s fatal shooting. New Delhi dismissed that allegation as “absurd”.

“If it was a case of rogue elements aggressively interpreting a general order to crack down on Khalistanis, it may be just a case of India being told to ‘back off and get your agents under control’,” said Walter Ladwig, an expert on South Asian security at the Royal United Services Institute in London.

“Whatever the case, it is certainly out of step with Modi casting himself as the teacher of the world,” Ladwig added, citing the Indian leader’s celebration of his country’s growing influence at the G20 talks.

The incidents have highlighted extremist elements among the Sikh diaspora in North America that Indian officials have long accused Canada and the US of tolerating.

“There are a lot of guys who participated in the Khalistani movement, terrorists by our definition, who are there in the US,” said Ajai Sahni, an Indian counter-terrorism expert. “Pannun is the most prominent voice at this juncture.”

India in 2020 designated Pannun a terrorist under the country’s Unlawful Activities (Prevention) Act. A year earlier, it declared Sikhs for Justice, the secessionist group where he serves as legal adviser, an unlawful association.

This month, Pannun made what Indian officials interpreted as a violent threat when he warned Sikhs that flying on Air India could be “life-threatening” after November 19. That date marked both the final of this year’s cricket World Cup in India and the birthday of former Prime Minister Indira Gandhi, who was assassinated by two Sikh bodyguards in 1984.

In a video filmed in front of a map of the proposed state of Khalistan, Pannun said that once India’s Sikh-majority Punjab state was “liberated”, its airports would be named after the bodyguards.

India’s anti-terrorism National Investigation Agency said this week it had filed a case against Pannun over the comments about Air India. Pannun has denied making a violent threat towards the airline.

His remarks stirred painful memories of the 1985 bombing of an Air India flight from Montreal to London that killed all 329 people on board. Two pro-Khalistan diaspora Sikhs were charged in the incident but later acquitted. 

This year, Pannun and Sikhs for Justice organised a Khalistan referendum in diaspora communities that was condemned by India’s government. The effort was accompanied by demonstrations, including outside India’s consulate in San Francisco, where protesters tore down the Indian flag.

Pannun in July told Indian media he was behind flyers posted outside the Sikh temple near Vancouver where Nijjar was killed that read “Kill India” and featured names and photos of Indian diplomats. This week, he accused India of “transnational terrorism”.

“Sikhs for Justice (SFJ) is using ‘Ballot’ to liberate Punjab while India is using ‘Bullets’ to stop the ongoing Khalistan Referendum — the motive behind India’s efforts to kill me,” Pannun told the FT. He added he would let the US government respond to the alleged threat.

The US justice department is debating whether to unseal its indictment or wait until Canada finishes its investigation into Nijjar’s murder. India’s external affairs ministry on Wednesday described Pannun’s case as “a cause for concern for both countries”, which was “already being examined”.

That response was a marked contrast to its blunt rejection of the Canadian allegations in September. New Delhi also retaliated by expelling most of Ottawa’s diplomats and suspending visa services for Canadians before quietly resuming them this week. 

The recent deaths of a number of Sikh activists abroad have drawn attention to alleged Indian overseas operations. 

In May, Paramjit Singh Panjwar, a Sikh militant leader, was shot dead in Lahore, Pakistan. In June, Avtar Singh Khanda, an activist and aide to the former fugitive Sikh leader Amritpal Singh, died in the UK of acute myeloid leukaemia. UK authorities refused a family request for an inquest into his death, a decision now being appealed.

“There is certainly a pattern, which has grown since the Canadian allegations,” said Avinash Paliwal, a reader in international relations at London’s School of Oriental and African Studies who has written about India’s foreign intelligence service, the Research & Analysis Wing. 

“It is something that the Five Eyes allies will be concerned about when it comes to India’s reliability as a partner. It may not end the relationship, but it will raise concerns about intelligence sharing,” he added.

Russia’s alleged attempt to assassinate double agent Sergei Skripal in the UK threw Moscow’s relations with western nations into turmoil in 2018. But in India, news of the alleged plots in Canada and the US has sparked little criticism of Modi, even from his political opponents.

Some commentators have accused the west of turning a blind eye to Sikh extremism and of double standards, pointing out Washington’s targeted killings of militants in other countries. 

“The official reaction is that the allegations are absurd, but the subtext is always that if we did it, it’s a good thing we did,” said Milan Vaishnav, director of the South Asia programme at the Carnegie Endowment for International Peace.

“There’s a popular embrace of India now being in a position to project power against its enemies, and a feeling that the west is overdosed on hypocrisy.”