The first group of South Koreans left Kabul Friday on special flights organized by the Afghan government.
They were to be transported to Mazar-I-Sharif or Herat, from where they were to leave the country by land transport.
Transport arrangements were also being made for group members in other Afghan cities.
General Sakhi Ahmad Bayani, a senior member of the Afghan Interior Ministry says the government is facilitating the arrangements because it was concerned for the group's safety.
He says the South Koreans traveled to several insecure locations throughout the country.
He says the South Korean embassy is helping transport the visitors out of Afghanistan.
More than 1,500 South Koreans entered Afghanistan several days ago for a so-called "peace march" in Kabul.
The program was organized by the South Korean-based Institute of Asian Culture and Development, a private charity that has close ties with South Korea's evangelical Christian movement.
Inside Afghanistan the group's arrival was immediately met with widespread suspicion.
Local Muslim leaders alleged the South Koreans were in Afghanistan seeking converts and demanded they be kicked out.
Afghanistan's constitution protects minority religious groups, including Christians, but proselytizing and missionary work are strictly forbidden.
Last March a local man was sentenced to death after he admitted that he had converted to Christianity.
The punishment sparked widespread international outrage and the man was later allowed to leave the country.
Western diplomats and security forces say they are closely monitoring the current situation along with South Korean officials.