Canada's defence minister Bill Blair has voiced concern over the measures taken by India, including the suspension of visa services for Canadians, and urged New Delhi to cooperate in the investigation of the killing of a Khalistani leader to uncover the truth.

Tensions have flared between India and Canada following Prime Minister Justin Trudeau's explosive allegations of "potential" involvement of Indian agents in the killing of Hardeep Singh Nijjar, 45, on June 18 in British Columbia. India had designated Nijjar as a terrorist in 2020.

India has angrily rejected the allegations as "absurd" and "motivated" and expelled a senior Canadian diplomat in a tit-for-tat move to Ottawa's expulsion of an Indian official over the case. India last week asked Canada to crack down on terrorists and anti-India elements operating from its soil and suspended visa services for Canadians.

"We received and believe we have very credible intelligence that causes us to be deeply concerned and the RCMP (Royal Canadian Mounted Police) have now initiated an investigation," Blair said in an interview with Canada's national public broadcaster CBC News on Sunday.

"One of the things I need to be very careful about is not confirming or identifying either the sources of any information we're acting on or the evidence or the type of evidence that forms part of that investigation, because the outcome of that investigation is critically important to Canada. It's also important to our allies in the world...," he said.

Asked whether he was concerned about some of the measures adopted by India, Blair said: "I am concerned about the measures that they're taking because we have a very significant (and) important Indo-Canadian population in this country, people who are connected to family and through business and other relationships to India."

He said that Canada recognises the impact that some of these measures may have and at the same time it's another reason why he placed such emphasis on the investigation that's taking place.

"So that we and the Indian government can know the truth and have the facts and then we can work together to resolve it in an appropriate way. And the only request we have made of our allies in India is that they cooperate fully in that investigation because its outcome is very important," the minister said.

Canada had been seeking deeper trade, defence and immigration ties with India before the “credible intelligence”, as Trudeau called it, was first raised with Canadian officials, according to Global News.

In a separate interview aired on Sunday on The West Block, Blair suggested Canada will continue to pursue partnerships like the Indo-Pacific strategy while the investigation into allegations continues, calling the relationship with India “important”.

“We understand that this can be, and has proven to be, a challenging issue with respect to our relationship with India,” he was quoted as saying by Global News.

“But at the same time, we have a responsibility to defend the law, defend our citizens, and at the same time make sure that we conduct a thorough investigation and get to the truth.”

If the allegations are proven true, Blair said, “there is a very significant concern that Canada will have with respect to the violation of our sovereignty in the murder of a Canadian citizen on Canadian soil.”

Blair said the Indo-Pacific strategy was still a critical one for Canada and has led to an increased military presence in the region and commitments for further patrol capabilities.

In his interview with CBC News, Blair said that every country in the world has strong trade interests in the Indo-Pacific region, as does Canada. "But at the same time, our engagement in that region or in any place of the world has to be based on those (international rules-based order) rules and Canada remains resolute in its commitment to uphold those rules," he added.