Canada announced this as Immigration Minister Jason Kenney issued an apology, observing that Canadian immigration officials should not have cast aspersions on India's institutions.
The incidents, he said, showed visa officers have too much latitude.
The Canadian High Commission, over the last few years, has denied visas to a number of senior serving and retired officials of the Indian armed forces and intelligence establishment, claiming that their organisations or they themselves have served in sensitive areas like Jammu and Kashmir and engaged in violence and human rights violations.
The incidents, some of which were recently highlighted in the media, sparked outrage in India with External Affairs Minister S M Krishna terming them unacceptable.
Going into a damage control mode, an embarrassed Stephen Harper government apologised and pledged to review immigration rules in an effort to repair relations, the Globe and the Mail said.
Canada's immigration law bars anyone who has committed war crimes or has engaged in terrorism, systematic or gross human rights violations, or genocide.
Canada and India, Kenney said in a statement, work closely together on security.
"The Government of Canada therefore deeply regrets the recent incident in which letters drafted by public service officials during routine visa refusals to Indian nationals cast false aspersions on the legitimacy of work carried out by Indian defence and security institutions, which operate under the framework of democratic processes and the rule of law," he said.
The apology came with a pledge that Canada will review its policy on declaring foreigners inadmissible. The incident, he added, "has demonstrated that the deliberately broad legislation may create instances when the net is cast too widely by officials, creating irritants with our trusted and valued international allies".
Canada is home to one million strong Indian diaspora.