Mr Trudeau had attended a conclave of Young Change Makers on February 24 where the map was reportedly shown incorrectly.
External Affairs Ministry Spokesperson Raveesh Kumar said India had taken up the matter with Canada.
"We had taken up the matter with the Canadian side," he said during a media briefing.
Mr Kumar said the Indian side was informed that the inaccurate depiction of the map happened at the conclave which was attended by the Canadian prime minister.
"We have been told that they do not imply endorsement or acceptance by the government of Canada," he said.
India's map shown at the event reportedly shown Pakistan Occupied Kashmir, Akshai Chin and Gujarat incorrectly.
Replying to another question, Mr Kumar said the visit of a Chinese dignitary here has been cancelled as he had to attend a meeting of China's Communist Party.
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