The pastor of the Mississauga Light Korean Presbyterian Church traveled regularly to North Korea for humanitarian missions and has always denied the allegations.
"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.
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 Koreanprison in a coma.
Canadian Prime Minister Justin Trudeau sent national security adviser Daniel Jean to North Korea to seek Lim's freedom.
Imprisoned since the month of February 2015 for acts subversive against the north Korean regime, the pastor has been released this week for medical reasons. The release came after diplomatic negotiation details of which are not known.
"Now more than ever, he's never felt more Canadian", the son said.
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The two nuclear powers have been steadily increasing their rhetoric, leading Freeland to condemn North Korea's actions but suggest it's time to reel in the verbal threats.
That could be an area of productive conversations with the United States, given the USA administration's focus on making it easier to do business, Freeland said.
"He is doing very well, considering everything he has gone through", he said.
"We stand by all of our allies very much including the United States".
Freeland said after meeting with members of the agricultural sector that the industry recommended the NAFTA talks could be used to reduce some of the red tape they face around cross-border trade.