The White House on Wednesday said it raised a report of a plot to kill a Sikh separatist on US soil "at the most senior levels" of the Indian government.
Earlier on Wednesday, the Financial Times, citing unnamed sources, reported US authorities had thwarted a plot that had targeted Gurpatwant Singh Pannun.
"Indian counterparts expressed surprise and concern. They stated that activity of this nature was not their policy," White House spokeswoman Adrienne Watson said in a statement obtained by Reuters.
"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,” she said.
Federal prosecutors also filed a sealed indictment against at least one suspect in the murder plot, the Financial Times reported.
India's Foreign Ministry has not yet commented on the report.
The FT reported that Mr Pannun declined to say whether federal authorities had warned him about the plot. However, he told FT he would let the US government respond "to the issue of threats to my life on American soil from the Indian operatives".
The US protest to New Delhi came after Indian Prime Minister Narendra Modi's state visit to the US in June, the newspaper reported.
The FT reported its sources did not say if the protest had led to the plot being abandoned, or if it was thwarted by the FBI.
The report came two months after Canada brought "credible" allegations linking India to the murder of Canadian citizen and Sikh separatist leader Hardeep Singh Nijjar in a Vancouver suburb this year.
The allegation sparked a diplomatic row between Canada and India, and New Delhi has rejected the allegations.
Mr Pannun is general counsel of Sikhs for Justice, an organisation that supports a Sikh state known as 'Khalistan' independent from India.
