Prime Minister Justin Trudeau said on Friday the Indian government's crackdown on Canadian diplomats was making normal life difficult for millions of people in both countries.

Trudeau spoke a day after Canada said it had withdrawn 41 diplomats following an Indian threat to unilaterally revoke their status. New Delhi is angry that Trudeau last month suggested Indian agents might have been involved in the June murder of a Sikh separatist leader in Canada.

"The Indian government is making it unbelievably difficult for life as usual to continue for millions of people in India and in Canada. And they're doing it by contravening a very basic principle of diplomacy," Trudeau said.

"It's something that has me very concerned for the wellbeing and happiness of millions of Canadians who trace their origins to the Indian subcontinent," he told reporters at a televised press conference in Brampton, Ontario.

Trudeau said the expulsion of some of Canada's diplomats will hamper travel and trade and pose difficulties for Indians studying in Canada.

Around two million Canadians, 5% of the overall population, have Indian heritage. India is by far Canada's largest source of global students, making up for roughly 40% of study permit holders.

The Indian foreign ministry earlier rejected the idea it had violated the Vienna convention on diplomatic relations.

"The state of our bilateral relations, the much higher number of Canadian diplomats in India, and their continued interference in our internal affairs warrant a parity in mutual diplomatic presence in New Delhi and Ottawa," it said in a statement. Canada now has 21 diplomats remaining in India.