Hyeon Soo Lim, 61, was arrested in 2015 for allegedly meddling in North Korean state affairs and sentenced to life in prison.
The South Korean-born pastor had been accused of subversive acts against Pyongyang, which Canadian authorities have strongly denied.
"A Canadian government delegation is currently in Pyongyang, DPRK, to discuss Pastor Lim's case," Trudeau spokesman Cameron Ahmad said.
"Pastor Lim's health and well-being remain of utmost importance to the government of Canada as we continue to engage on this case," he said. "As this is an active case, we will not provide further comment at this time."
Lim's family told local media they have become increasingly worried about his welfare since the death of an American student in June just days after he had been released from a North Korean prison.
At the time of his arrest, other members of the close-knit circle of ethnic Korean missionaries in Canada and the United States called Lim one of the most influential Christian missionaries operating in North Korea.
He had visited the country dozens of times, working with orphanages and nursing homes.
But some projects he worked on, including a noodle plant and flour mills, were linked to associates of Jang Song-Thaek, the purged uncle of leader Kim Jong-Un. Jang Song-Thaek was arrested and executed for treason in December 2013.
Lim told CNN last year that he now spends his days in prison digging holes.
Pyongyang views foreign missionaries with deep suspicion, though it allows some to undertake humanitarian work.
A number of Christian missionaries -- mostly ethnic Koreans who are US citizens -- have been arrested in the past, with some of them only allowed to return home after intervention by high-profile US political figures.
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