Canadian officials are investigating charges that the Indian government has carried out illegal intelligence operations in Canada that may be linked to a series of violent incidents within the local Sikh community.

Sources here confirmed tonight a report in today's Toronto Globe and Mail that Canadian officials believe the Indian government agents have operated covertly here for more than three years and seemed to be working to discredit Canadian-based groups pressing for a separate Sikh homeland in India.

Indian High Commissioner S.J.S. Chatwal vehemently denied the report, saying, "The whole thing to our mind is completely baseless and goes to almost being nonsense."

But Canadian External Affairs Ministry spokesman Sean Brady, in a carefully worded statement, made no similar blanket denial.

"We have made it clear on previous occasions that any improper activity by foreign representatives from any country which would interfere in the lives of Canadian citizens and residents, if confirmed, is inappropriate," Brady said. "We continue to monitor these matters closely through the concerned agencies of the Canadian government, and we would take appropriate actions as required."

Another official statement, by the Royal Canadian Mounted Police, disputed only one part of the extensively detailed article. The Mounties said there was no "substance or foundation" to the assertion in the Globe and Mail that Canadian investigators now believe Indian government agents may have been responsible both for the crash of an Air- India jet off the coast of Ireland last June and the explosion on the same day of a suitcase at Tokyo's Narita airport.

Two baggage handlers were killed in Japan and all 329 passengers and crew perished in the Air-India crash. Both the luggage and the Air-India flight had originated in Canada.

Canadian officials were known to be probing several other allegations in the newspaper account, which included assertions that:

*At least four Indian government intelligence operatives also worked under diplomatic cover at Indian consulates in Toronto and Vancouver.

*Some of those agents may have been responsible for fomenting violence during a Sikh rally in Toronto three years ago in which a police constable of Indian origin was shot and wounded.

*Other agents, posing as religious zealots, had infiltrated and taken over one Sikh organization and turned it into a fanatical group.

Sources here indicated that the aim of the purported Indian intelligence activity may have been to create divisions among separatists and to outflank the mainstream separatist movement with extremist groups.

Indian diplomats have complained privately in the past that Canadian officials have not done enough to protect them from physical attacks by separatists and have indicated that they did not believe either U.S. or Canadian officials had been sufficiently aggressive in pursuing Sikh terrorism.

At the Commonwealth conference in September, Indian Prime Minister Rajiv Gandhi expressed to Prime Minister Brian Mulroney his country's concerns about the activities of Sikh separatists in Canada. The two agreed tentatively to an extradition treaty next year that would be retroactive. The matter is expected to be discussed further when Canadian Secretary for External Affairs Joe Clark visits India next month.

Sources here indicate that Canadian officials have been displeased for some time about the reported Indian intelligence operations but have been reluctant to move to shut them down because of concern that they might appear to the public to have been linked to the two airline disasters in June.

Chatwal said that the only time Indian government intelligence agents had come to Canada was shortly after the two airline incidents. He said the "three or four" who came stayed for less than two weeks and were involved only in exchanging information with Canadian investigators probing the incidents.

Jerry Cummings, spokesman for the Canadian Security Intelligence Service, declined to comment on Chatwal's remarks and said that he would neither confirm nor deny that an investigation had been launched into the activities of Indian government agents here.