A Canadian pastor who was imprisoned in North Korea for more than two years quietly returned to his home in a Toronto suburb on Saturday following a long journey on a private government jet via Japan.

Hyeon Soo Lim, formerly the senior pastor at one of Canada's largest churches, had disappeared on a mission to North Korea in early 2015. He was sentenced to hard labour for life in December 2015 on charges of attempting to overthrow the Pyongyang regime.

News of his release surfaced on Wednesday, when North Korea's KCNA news agency said Lim was being let go on humanitarian grounds, suggesting his health was poor.

The announcement came amid heightened tensions between Washington and Pyongyang, though authorities have not said there is any connection between his release and efforts to defuse the standoff over North Korea's nuclear programme.

The pastor's son James Lim said his dad was happy to be back home in Canada, stopping for coffee and a donut at Canada's popular Tim Horton's coffee chain on his way home from the airport.

The family asked the public to respect their privacy, allowing him to rest for a day and catch up with family before appearing in public on Sunday to attend services at his church.

James Lim said his dad was in "good health," but noted that the family planned to arrange for extended medical attention, including checkups.

"He is doing very well, considering everything he has gone through," he said.

The family thanked the Canadian government for helping secure his Lim's release. They declined to provide details on negotiations with the North Koreans.

"It's a delicate dance. There's a lot of complexity to it," James Lim said.

He added that getting the pastor home took on increased urgency in June, following the death of Otto Warmbier, an American student who died days after being released from a North Korean prison in a coma.

The Canadian government issued a statement saying it joined Lim’s family and congregation in celebrating his homecoming.

“Canada has been actively engaged on Mr. Lim’s case at all levels, and we will continue to support him and his family now that he has returned," the statement said.