AFP reports some 400 Koreans have been already flown to the northern cities of Mazar-e Sharif and Herat, from where they are expected to leave the country by land.
South Korea's Yonhap news agency quotes an official of the Foreign Ministry in Seoul as saying both governments would force all Koreans to leave the country.
The move follows the decision by the Afghan government to cancel a three-day "peace festival" organized by South Korean Christians that was due to start on August 5.
Muslim clerics had accused the South Koreans of coming to the country to proselytize.
Up to 1,000 South Koreans had already arrived in Afghanistan for the festival, which was to include a medical conference and two soccer matches. Its organizers have denied the accusations of evangelism brought against them.