“When we checked again today, the refugees were gone,” he said. “We fear the worst.”

In Seoul, Roh Kyu-deok, a Foreign Ministry spokesman, said that South Korea was “closely monitoring” the case.

“We’re making diplomatic efforts with the related country so that the defectors will not be forcibly repatriated,” Mr. Roh said. “We have been consistently appealing for North Korean refugees to be sent where they want to go out of humanitarian consideration.”

Hua Chunying, a spokeswoman for the Chinese Foreign Ministry, said on Tuesday that she was unaware of details of the case. But she said that China handled such matters in accordance with domestic and international law and humanitarian principles.

Most of the 30,000 North Koreans who have fled to the South since a devastating famine the 1990s have traveled through China. Beijing treats North Koreans fleeing their country as illegal migrants, not as refugees, and often deports them back to North Korea despite defectors’ testimonies that those returned are often sent to prison camps.

Mr. Kim, whose Caleb Mission church in Cheonan, south of Seoul, has helped hundreds of North Koreans resettle in the South, said he knew the identities of only the three people he had helped. The boy’s father, who fled to South Korea two years ago, had saved the money to help his family leave their town, which suffered heavily during a flood last year, Mr. Kim said.