The Joe Biden administration, too, confirmed that the US, at the senior most levels, raised the concern with India and expected those deemed responsible to be held accountable. India, according to the US, was surprised and concerned when the issue was raised, and told Washington DC that this was not government policy and will investigate the matter.

The remarks by the ministry of external affairs (MEA) came in response to the report in the London-based newspaper which also suggested that the US warned India against any involvement in a plot to kill Pannun, a Sikh extremist the government of India officially designated as a terrorist but who also happens to be a dual American and Canadian citizen.

“During the course of recent discussions on India-US security cooperation, the US side shared some inputs pertaining to nexus between organised criminals, gun runners, terrorists and others. The inputs are a cause of concern for both countries and they decided to take necessary follow-up action,” MEA spokesperson Arindam Bagchi said.

Bagchi added that India took such inputs seriously as it impinged on Indian “national security interests as well”. “Issues in the context of US inputs are already being examined by relevant departments.”

The FT report said it was unclear whether the developments led the plotters to abandon their plan of killing Pannun, or “whether FBI intervened and foiled a scheme”. “One person familiar with the situation said the US protest was issued after Prime Minister Narendra Modi made a high-profile state visit to Washington in June,” the report added.

The development came two months after Canada said there were “credible” allegations linking Indian agents to the murder of another Sikh separatist leader, Hardeep Singh Nijjar, in a Vancouver suburb. New Delhi has denied the charges and said there was no proof to back the allegations.

On Wednesday, FT reported on the American message to India, adding that US federal prosecutors have also filed a sealed indictment against “one of the perpetrators of the plot” in the New York District Court. The US justice department hasn’t unsealed the indictment.

“We are treating this issue with utmost seriousness, and it has been raised by the US government with the Indian government, including at the senior most levels. Indian counterparts expressed surprise and concern. They stated that activity of this nature was not their policy,” US National Security Council spokesperson Adrienne Watson said in a statement.

The statement came in response to a question about the allegations, whether the US can confirm either having such a conversation with India or whether it has any specific asks from India on the issue.

“Based on discussion with senior US government officials, we understand the Indian government is further investigating this issue and will have more to say about it in the coming days. We have conveyed our expectation that anyone deemed responsible should be held accountable,” the statement added.

An earlier statement by an NSC spokesperson also underlined that the safety and security of American citizens was “paramount”.

The US State department did not comment on the issue “We do not comment on diplomatic, law enforcement, or intelligence discussions with our partners. Upholding the safety and security of US citizens is our highest priority,” a spokesperson said.

In September, Canada’s Prime Minister Justin Trudeau, on the floor of the Canadian parliament, said that there were “credible allegations” linking agents of the government of India to the killing of Nijjar, another designated terrorist who happened to be a Canadian citizen.

Trudeau’s charge led to a major diplomatic rupture between Canada and India, besides raising questions in other western capitals including Washington, which is both Ottawa’s closest ally and a fellow member of the Five Eyes alliance, the world’s premier intelligence network.

The US asked India to cooperate with Canadian authorities and expressed its concern. India termed Trudeau’s allegations absurd, said this was not government policy, and added that if Canada had something specific to offer, Indian would be willing to look at it. New Delhi also used the moment to expose what it saw as Ottawa’s permissive environment for terror, violence and organized crime under the rubric of free speech.

Both Pannun and Nijjar are pro-Khalistan separatists with a history of supporting secessionism, inciting violence, and mobilising funds for extremism. Just this month, on November 4, Pannun, the head of the banned outfit Sikhs for Justice, warned Sikhs against travelling on Air India flights on and after November 19, and threatened that Air India would not be allowed to operate. This week, the National Investigation Agency (NIA) filed a case against Pannun under various sections of Indian Penal Code (IPC) and Unlawful Activities Prevention Act.

India and the US have been careful not to allow Canada’s allegations to interrupt the momentum in bilateral ties.

The relationship has built on the momentum of Prime Minister Narendra Modi’s state visit to Washington DC in June. In September, President Joe Biden visited Delhi for the G20 Summit where US support played a key role in helping the presidency arrive at the leaders’ declaration. External affairs minister S Jaishankar then visited Washington where he met national security adviser Jake Sullivan, secretary of state Antony J Blinken, secretary of defence Lloyd Austin and is understood to have had private conversations with top US intelligence community figures.

In November, both Blinken and Austin visited Delhi for the annual 2+2 dialogue to deepen strategic and defence ties. And last week, Indian commerce and industry minister Piyush Goyal was in San Francisco, where he participated in the Indo-Pacific Economic Framework ministerial and represented India, an invited guest country, at the APEC summit.

US ambassador to India Eric Garcetti has also said that Modi invited Biden to be the chief guest at the Republic Day ceremony on January 26 next year, where he may attend the Quad Leaders’ Summit. While there is no official confirmation of the visit, those familiar with the conversations suggest that it remains on the table and will be contingent on Biden’s schedule and domestic and international commitments.