However, Toronto rejected all the allegations against Hyeon, who served at one of the largest churches in Canada.
The Canadian delegation is led by Daniel Jean, the national security adviser to Prime Minister Justin Trudeau.
"Strategically, North Korea perhaps hopes to engender some goodwill from Canada as tensions rise", said Charles Burton, a former Canadian diplomat in China.
His January 2015 arrest came just a couple months after the release of missionary Kenneth Bae, who faced similar charges as the longest-serving U.S. prisoner in North Korean history.
"We want to thank the global community for the continued prayers and support and we also ask that the world does not forget the people of North Korea", the statement read.
The state-run news agency said 62-year old Heyon Soo Lim was released for "humanitarian reasons" on Wednesday.
"So far, it has been confirmed that government officials and a doctor are accompanying Reverend Lim", said the source, speaking on condition of anonymity because they were not authorised to speak to media.
After the death of Otto Warmbier in June, an American citizen detained in North Korea and only released when he had already suffered brain damage, Trudeau has faced increased calls to pressure Pyongyang to free the Canadian minister. Warmbier died in a Cincinnati hospital just days after he was released in a coma.
North Korea's highest court said the South Korean-born pastor had attempted to overthrow the government and undermine its social system with "religious activities" for the past 18 years.
But Lim isn't the only point of concern for Trudeau in dealing with North Korea, whose aim to develop nuclear missiles capable of reaching across the Pacific has Canadians anxious they are in range.
A senior Canadian official said their trip was exclusively linked to Lim's condition and was not related to the increasing global tensions with the state.