Sejong City, 120km (75 miles) from Seoul, was to become the new capital, but a high court ruled this to be illegal.
Moving some government offices there is a way of spreading economic benefits and easing congestion, proponents say.
But critics argue that the move will only result in inefficiency.
The initial proposal to make Sejong City South Korea’s new capital was made in 2002, but the Constitutional Court rejected this in 2004.
At least 36 government agencies and offices are scheduled to transfer to Sejong City by 2015. Thousands of civil servants are expected to make the move there over the next few years.
But key offices like the president’s office, and the defence and foreign ministries, are to remain in Seoul.
Aside from the economic benefits, Sejong City is also seen as a good security move because it is further away from the border with North Korea.
“There are worries that the division of central government bodies can cause inefficiency,” Prime Minister Kim Hwang-Sik was quoted by Agence France-Presse news agency as saying.
“We will try hard to quell such concerns and to forge a good balance and co-ordination among the agencies.”
One government official interviewed by the BBC’s Lucy Williamson, however, complained that the relocation would mean a two-hour drive back to Seoul for meetings.