Harper is usually the one to urge vigilance over extremism and terrorism as he travels the world meeting with his counterparts but on Tuesday the shoe was on the other foot during a meeting in India's capital with India's minister of state for external affairs Preneet Kaur.
"Prime minister, there was another area of great concern for us, which was the revival of anti-India rhetoric in Canada, and I am from the state of Punjab, which we are very happy you will be visiting," Kaur said during a morning meeting.
"We have after very hard times got a good situation of peace and progress back in Punjab and in India and we would like that to continue, so it does concern us I think, and we do appreciate very much that you have very been forthright and open about your stand on this."
Indian Prime Minister Manmohan Singh touched on the issue again during an evening ceremony. The two nations announced they had finally concluded their talks on how to implement a nuclear co-operation agreement, meaning Canadian companies might starting shipping uranium and other products to India in the near future.
"India and Canada are nations built on shared values that celebrate democracy, inclusiveness and diversity," said Singh. "We have similar concerns in combating terrorism, extremism and radicalism."
The issue of internal extremism has been one that has shaken India to the core over the past several decades — former prime minister Indira Gandhi was murdered by her own Sikh bodyguards after a string of events sparked by fundamentalists seeking their own separate, fundamentalist nation they would call Khalistan.
Canada too has been rocked by related terrorism. Police believe the bombing of a 1985 Air India flight that killed 331 people was orchestrated by Sikh extremists based in Canada.
Pockets of pro-Khalistan support are still visible in the Indo-Canadian community. The flags and seals of the movement appear at parades and at Sikh places of worship or gurdwaras. Hundreds of Sikhs protested on Parliament Hill in March against the death row sentence of an acknowledged Sikh terrorist, Balwant Singh Rajoana.
Harper responded to India's concerns by saying that Canada is a supporter of a united India.
"This is a view that is shared not just widely in Canada but very widely and very mainstream among our Indo-Canadian community," Harper said told Kaur during their meeting.
"We have over a million people who trace their origins to the Indian subcontinent and among my very large delegation on this trip are a considerable number of prominent Indo-Canadians, and certainly the support for the great progress India has made over the past generation is virtually universal in this community."
But Harper and his government have had to tread carefully when wading into the issue of potential Sikh extremism or even terrorism. The Conservative party enjoys substantial support from the Indo-Canadian community, some of whom feel they are being unfairly stereotyped by India.
British Columbia MP Nina Grewal said she doesn't really understand where the suggestion comes from that Canada has a Sikh extremist problem.
"Well, 99.9 per cent of the people are very peace-loving people ... I haven't witnessed anything of this type in Canada," Grewal said.
Foreign Affairs Minister John Baird had to smooth ruffled feathers earlier this fall after making comments about fighting terrorism during a visit to India.
"I want to make absolutely clear that at no point during my visit did I make generalized assertions about any community in Canada, including but not limited to Canadian Sikhs," Baird wrote in an open letter.
The federal opposition in particular has taken up the cause of Canadian Sikhs, who want more recognition of the November 1984 massacre of more than 3,000 Sikhs in India.
The remains of murdered Sikhs in razed villages were uncovered as recently as last year and many believe the Indian government has not done enough to bring the perpetrators to justice.
The massacre occurred in the aftermath of Indira Gandhi's assassination. The bodyguards were believed to have been retaliating for a bloody military operation in June of that same year aimed at extricating Sikh militants from the Golden Temple in Amritsar.
Groups such as the World Sikh Organization and the Canadian Sikh Congress argue that the community has a right to engage in a peaceful dialogue about a sovereign homeland and the Indian government is meddling in the affairs of Indo-Canadians.
Another group, Sikhs for Justice, recently called on Harper to advocate for human rights for Sikhs while in India.
NDP Leader Thomas Mulcair referred to the events of 1984 as "pogroms" in a recent release.
"The victims and survivors of 1984 have waited too long for recognition of their plight and frustration," Mulcair said. "Rehabilitation and support for the broken families, especially the widows, must be prioritized."
Harper is set to visit the Punjabi capital of Chandigarh on Wednesday.
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