The North Koreans have been taken to a rebel camp northeast of Tachilek, a town along the border between Myanmar and Thailand, over the past nine years, Pastor Kim Hee-Tae told AFP.
The refugees were caught while attempting to travel on their own through rebel-held territory to Thailand in order to defect to South Korea after fleeing their poverty-stricken homeland.
"We're in a great dilemma over how to rescue them", Kim said, adding the rebels were asking for $5,000 ransom for each of the hostages.
He said NGOs were unable to launch a campaign to raise the money or to ask for Seoul to intervene as the hostage takers were extremely publicity shy.
"We need very quiet negotiations to pull it through", he said.
About 80 percent of the North Koreans were women and were forced to work at alcohol manufacturing or drug processing plants. "Some of them are forced into prostitution", he said.
Male captives were used to grow poppies.
A South Korean foreign ministry official said the ministry was investigating the case.
Myanmar is the world's second largest producer of opium -- the raw ingredient for heroin -- after Afghanistan, accounting for 10 percent of global production, according to UN data.
Since the end of the Korean War in 1953, some 25,000 North Korean refugees have escaped and settled in the South.
Most begin their journey by crossing into China, where they face repatriation if caught.
They then try to reach a second country, with Thailand the most popular choice, from where they generally seek permission to resettle in South Korea.
Those who are caught and deported back to the North face severe punishment, including being sent to a labour camp, rights groups say.
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