About 2,000 Koreans say they came to Afghanistan for a "peace festival and educational and entertainment programmes".
Kang Sung Han, a member of the visiting Korean team in Kabul, said on Thursday: "Yes, yes, we have been told to leave Afghanistan because of security concerns".
Han said the Koreans in Kabul have been confined to their accomodation while those outside the capital are preparing to leave the country.
A foreign ministry official in Seoul said the Afghan government had already deported 35 of the evangelical Christians in the past few days and would soon send home another 900.
"The government has started the process of deporting the South Koreans, but securing available planes to take them back to South Korea would not be a easy job," the official said.
Hundreds of Islamic clerics rallied in an ancient mosque in a the north of Afghanistan on Wednesday to demand the Koreans' expulsion after accusing them of trying to spread Christianity.
In February, thousands demonstrated against the release of a man facing the death penalty for converting to Christianity from Islam.
The man, Abdur Rahman, was released from prison and left for Italy after international condemnation of the sentence by Western leaders and Pope Benedict.