Visa service provider BLS posted a message from India’s mission blaming “operational reasons” for the decision.
Tensions flared this week after Canada said it was investigating “credible allegations” linking India with the murder of the separatist leader.
India angrily rejected the allegation calling it “absurd”.
Analysts say relations between the countries, which have been strained for months, are now at an all-time low.
The message about the suspension of visas was first posted on the BLS website on Thursday.
“Important notice from Indian Mission: Due to operational reasons, with effect from 21 September 2023, Indian visa services have been suspended till further notice,” it read.
India’s foreign ministry refused to comment on the matter and asked the BBC to refer to the BLS website.
The move comes a day after India issued an advisory urging its citizens travelling to or living in Canada to “exercise utmost caution” in view of the “growing anti-India activities and politically-condoned hate crimes and criminal violence in Canada”.
Canada has 1.4 million people of Indian origin, making up 3.7% of the country’s population, according to the 2021 census. India also sends the highest number of international students to Canada – in 2022, they made up 40% of total overseas students at 320,000.
On Wednesday, Delhi said that some recent threats were directed at its diplomats and some Indians “who oppose the anti-India agenda”.
Canadian Prime Minister Justin Trudeau said on Monday that intelligence agencies were investigating whether “agents of the government of India” were involved in the killing of Hardeep Singh Nijjar, a Canadian citizen – India had designated him a terrorist in 2020.
Nijjar was shot dead in his vehicle by two masked gunmen outside a Sikh temple on 18 June in British Columbia.
“Any involvement of a foreign government in the killing of a Canadian citizen on Canadian soil is an unacceptable violation of our sovereignty,” Mr Trudeau told the Canadian parliament on Monday.
India reacted strongly, saying that Canada was trying to “shift the focus from Khalistani terrorists and extremists” who had been given shelter there.
The Indian government has often reacted sharply to demands by Sikh separatists in Western countries for Khalistan, or a separate Sikh homeland.
The Khalistan movement peaked in India in the 1980s with a violent insurgency centred in Sikh-majority Punjab state.
It was quelled by force and has little resonance in India now, but is still popular among some in the Sikh diaspora in countries such as Canada, Australia and the UK.
Canada is home to the largest Sikh population outside India, with around 780,000 Sikh people – more than 2% of the country’s population. It has seen several pro-Khalistan protests and demonstrations.
In June, reports said India had raised a “formal complaint” with Canada about the safety of its diplomats there.
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