Relations With Canada Passing Through Difficult Phase: Jaishankar

India on Sunday said its relationship with Canada is passing through a difficult phase and there had been "continued interference" by Canadian personnel in New Delhi's internal affairs.

The Indian government is angry that Canadian Prime Minister Justin Trudeau last month suggested Indian agents might have been involved in the June murder of a Sikh separatist leader in British Columbia. India denies the allegation.

"The relationship right now is going through a difficult phase. But I do want to say the problems we have are with a certain segment of Canadian politics and the policies which flow from that," India’s foreign affairs minister S. Jaishankar said at an event.

Canada had to withdraw 41 of its diplomats from India on Thursday as New Delhi decided to unilaterally revoke their official diplomatic status.

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

Jaishankar said India had invoked diplomatic parity under the Vienna Convention, "because we had concerns about continuous interference in our affairs by Canadian personnel".

"We haven't made much of that public. My sense is over a period of time more stuff will come out and people will understand why we had the kind of discomfort with many of them which we did”, Jaishankar said.

Canada’s Foreign Minister Melanie Joly said last week India’s stand was unreasonable and unprecedented and clearly violated the Vienna Convention on diplomatic relations.

Jaishankare also said India had stopped issuing visas in Canada a few weeks ago due to concerns over the safety and security of its diplomats in going to work. He said India would resume the issuance of visas if there was progress in the safety of its diplomats working there.

Around two million Canadians, or 5 per cent of the population, have Indian heritage. India is by far Canada's largest source of overseas students, making up roughly 40 per cent of study permit holders.