There was interference in New Delhi's affairs by Canadian personnel, said S Jaishankar explaining the downsizing of Canadian diplomatic presence in the country, adding that India has "problems with certain segment of Canadian politics".
Canada has already withdrawn 41 of its diplomats from India.
"Parity is very much provided for by the Vienna Convention, which is the relevant international rule on this. In our case, we invoked parity because we had concerns about continuous interference in our affairs by Canadian personnel," Mr Jaishankar said, rejecting the idea that India had violated the Vienna convention on diplomatic relations.
"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," the Minister said.
The comment comes just days after Canadian Prime Minister Justin Trudeau said that the Indian government's crackdown on Canadian diplomats was making normal life difficult for millions of people in both countries.
"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," said Mr Jaishankar.
Canada is home to some 770,000 Sikhs, who make up about two per cent of the country's population, with a vocal minority calling for creating a separate state of Khalistan. The Sikh separatist movement is largely finished within India, where security forces used deadly force to put down an insurgency in the state of Punjab in the 1980s.
New Delhi is angry that Trudeau last month suggested Indian agents might have been involved in the June murder of a Sikh terrorist in Canada.
Canada has called for India to cooperate in the investigation but New Delhi has rejected the allegations and taken countermeasures, such as shutting down visa services for Canadians. Also, Canada is yet to provide any public evidence to support the claim about the killing of Nijjar.
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.
"Right now the big concern which people have is on visas. Some weeks ago, we stopped issuing visas in Canada because it was no longer safe for our diplomats to go to work to issue visas. So their safety and security was the primary reason we had to temporarily stop the issue of visas. We're tracking it very closely," he said.
"My hope, my expectation is that situation would improve in the sense that our people would have greater confidence in being able to do their basic duty as diplomats. Because ensuring safety and security of diplomats is the most fundamental aspect of the Vienna Convention. And right now that is what has in many ways been challenged in Canada that our people are not safe, our diplomats are not safe. So if we see progress there, I would like very much to resume the issue of visas," the Minister added further.
