Three Indian men were charged in the brazen slaying of a Sikh separatist on Canadian soil, the police said on Friday, a killing that set off a diplomatic clash with New Delhi after Prime Minister Justin Trudeau blamed “agents of the government of India” for orchestrating the shooting.

India’s government called the claim “absurd” and took steps that led Canada to withdraw more than 40 of its diplomats from the country. But amid the denials, Canada said it had a “smoking gun,” supported by information from the United States. And a federal indictment in New York linked the Indian government to another murder-for-hire-plot against another Sikh separatist.

The three men were arrested in Edmonton, Alberta, and charged with first-degree murder and conspiracy to commit murder in the killing of the Sikh nationalist, Hardeep Singh Nijjar, in June, the Royal Canadian Mounted Police said. The suspects — Karan Brar, 22; Kamalpreet Singh, 22; and Karanpreet Singh, 28 — had been living in Canada for three to five years but were not permanent residents of Canada, the police said.

“This investigation does not end here,” Superintendent Mandeep Mooker, head of the Integrated Homicide Investigation Team for the Mounties, said at a news conference on Friday. “We are aware that others may have played a role in this homicide, and we remain dedicated to finding and arresting each one of these individuals.”

Several other investigations are ongoing, including into any possible involvement by the Indian government in Mr. Nijjar’s killing, Assistant Commissioner David Teboul said at the news conference. He also said, without providing further details, that the relationship with India in investigating the killing had been challenging.