The three-day event that starts in Kabul on Saturday comes amid an increase in violence, a foreign ministry official said in Seoul.
Speaking on telephone, the official, who asked not to be named, said: "We are very worried about their safety. It is just like jumping into a fire."
But the Christians from evangelical Protestant groups have said that the South Korean government is overreacting about the danger of their trip.
They say the event in Kabul is cultural and not an evangelical movement aimed at spreading the Christian faith.
"The peace festival will not be dangerous. The Afghan government has welcomed our attendance at the event"
Institute of Asian Culture and Development
Choi Han-woo, head of the Institute of Asian Culture and Development (IACD), which is sponsoring the event, had told Reuters last month that "the peace festival will not be dangerous. The Afghan government has welcomed our attendance at the event."
Representatives from the groups were not immediately available for comment on Tuesday.
In 2004, some 2,000 South Korean Christians from IACD shrugged off government requests to avoid the Middle East during the Iraq war and went to Israel to join a peace march between the biblical cities of Bethlehem and Jerusalem.
None of them was attacked during their visit.
South Korean evangelical groups have sent missionaries to various parts of the Middle East, including areas where there has been armed conflict.