The agency said the decision to send Yi So-yeon, 29, to the International Space Center instead of Ko San was made following requests from the Russian side.
"The main reason for the change is based on two consecutive violations of training protocol by Ko," the news agency quoted Lee Sang-mok, the head of the space technology bureau with the South Korean Ministry of Education, Science and Technology, as saying.
The official said that last month Ko acquired pilot's instructions that he was not authorized to read, as his main mission in space is to carry out scientific experiments.
The Russian Space Agency did not comment on the change, saying it was up to South Korea to make such decisions.
Yi is set to travel to the ISS on board Russia's Soyuz spacecraft on April 8. She will become the second Asian woman in space after Japan's Chiaki Mukai, who made two space flights in 1990s.
