India has suspended visa applications by Canadian nationals, according to a third-party processor used by the Indian government, a sharp escalation in the diplomatic conflict that has followed Canada’s claim that Indian agents were behind an assassination in June on Canadian soil.

The processing company, BLS International, issued the notice on Thursday. Contacted by The New York Times, a spokesman for India’s foreign ministry said he could not confirm that visa processing had been halted. A ministry news briefing was scheduled for Thursday afternoon.

India and Canada have been locked in a bitter clash since Monday, when Prime Minister Justin Trudeau said in a speech to Parliament that Canada’s intelligence services had information linking the Indian government to the killing of a Sikh separatist in British Columbia on June 18.

The Indian government on Tuesday forcefully rejected the claim that it had been involved in the assassination of the Sikh Canadian citizen, Hardeep Singh Nijjar, and accused Canada of harboring terrorists who are seeking to carve a Sikh homeland out of India’s territory.

India then moved to expel a high-ranking Canadian diplomat from New Delhi. Canada had expelled an Indian diplomat — described as the head of New Delhi’s intelligence agency in Canada — the day before.

On Wednesday, the Indian foreign ministry advised Indian citizens living in or traveling to Canada to “exercise utmost caution” because of what it described as an increase in “anti-India activities and politically condoned hate crimes and criminal violence in Canada.”

“Recently, threats have particularly targeted Indian diplomats and sections of the Indian community who oppose the anti-India agenda,” the advisory said, adding that Indian nationals should avoid traveling to regions and sites in Canada that had seen such incidents.

Dominic LeBlanc, Canada’s minister of public safety, dismissed India’s travel warning in remarks to reporters in Ottawa.

“People can read into that what they want,” he said. “Canada is a safe country. What we’re doing is ensuring there’s an appropriate criminal investigation into these circumstances.”

The Canadian government has yet to release any details about its intelligence findings in Mr. Nijjar’s death, saying that doing so could damage the police investigation and reveal the country’s intelligence-gathering methods. Canada has asked for India’s assistance in the inquiry.

“We are not looking to provoke or escalate,” Mr. Trudeau told reporters on Tuesday. “We are simply laying out the facts as we understand them, and we want to work with the government of India.”

Relations between India and Canada have plunged this week to what officials and analysts call the lowest point in history after years of simmering tension.

The Indian government has long accused Canada and other Western nations of inaction as extremist Sikh groups in the Indian diaspora — including the one led by Mr. Nijjar — have supported a secessionist movement that threatens India’s sovereignty.

Canada has said that it respects the right of all of its citizens to freedom of speech in advocating political causes. Indian officials say that Canadian politicians are reluctant to curb Sikh extremism because of the lobbying sway of the group, the largest population of Sikhs outside India.

Officials in India have accused Canada, Britain, the United States and Australia of standing by as those pushing for what is known as Khalistan, the independent nation that Sikh secessionists want to establish in the Punjab region of India, have vandalized Indian diplomatic missions and threatened Indian diplomats.

As tensions soar, Canada said on Wednesday that it was pulling some of its diplomats out of India to ensure their safety. It said that some diplomats had received threats on social media.