Hyeon Soo Lim, 60, has been the head pastor of Light Korean Presbyterian Church in Toronto, Canada for 28 years.
According to church spokeswoman Lisa Pak, Pastor Lim had made hundreds of visits to the country since 1997 to help oversee various humanitarian projects. She said she hasn't been heard from him since January.
Ms Pak also said Canadian officials had confirmed his incarceration to Pastor Lim's family, and that she could not speculate as to why Mr Lim had been imprisoned.
Revd Chun Ki-Won, who directs a South Korean Christian organisation which helps North Korean refugees, has called Mr Lim was one of the most influential missionaries operating north of the border.
The Open Doors Word Watch List currently rates North Korea the worst country in the world for Christian persecution.
