"I raised issue of Khalistan as its the primary issue, as there is money coming in from various countries including Canada," Captain Amarinder Singh said after meeting the Canadian PM.
The meeting took place at the Taj hotel after Mr Trudeau, his family and ministers visited the Golden Temple, the holiest Sikh shrine, and the Partition museum.
Amarinder Singh, also known as the Captain, had last year said he was "not interested" in meeting Canadian ministers, making no bones about his criticism of what is perceived as Canada's soft approach to Sikh extremist groups campaigning for a Khalistan state.
He had made the comments to Shekhar Gupta in April during the visit of Canada's Defence Minister Harjit Sajjan Singh.
Asked whether he would meet Harjit Sajjan Singh in Punjab, the Captain had replied: "No. I am not going to go. I'll put some minister in-charge... I'll tell you on a matter of principal, I don't agree on this. There are five ministers there who are Khalistanis and I am not interested in meeting any Khalistanis."

Punjab Chief Minister Captain Amarinder Singh arrives at the Taj Swarna in Amritsar for his meeting with Canadian PM Justin Trudeau
In Mumbai, Prime Minister Trudeau emphasised his support for a united India. "We of course reject violence and hate speech or hateful speech, but at the same time I can reassure everyone that my position, that Canada's position has not changed. We support one united India," he said, replying to a question.
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The 46-year-old prime minister arrived in India on Saturday evening on a week-long visit, along with his wife Sophie Gregoire Trudeau and three children.
Justin Trudeau and his family visited the Golden Temple in Amritsar.
So did the Canadian premier, who, asked whether he thought he had been snubbed by PM Modi, told reporters on Monday: "I have met with the prime minister in various places around the world and looking forward to sitting down with him on Friday."