The remains will be examined for identification before being buried in the national cemetery in the city.
According to the South Korean defense ministry the remains of more than 1,700 soldiers have been recovered since the project was launched seven years ago.
Kim Sung-koo, a ministry official, said that as inter-Korean relations improved Seoul planned to seek cooperation with authorities in Pyongyang in excavating the remains of South Korean soldiers lost in the North.
Some 30 per cent of the missing remains of South Korean soldiers are believed to be in the North, he said.
Nearly 137,900 South Korean troops were killed and more than 19,300 servicemen are still listed as missing.
The Korean War, which began in June 1950 when North Korea invaded the South, ended in an armistice in 1953 but both countries are still technically at war.
Roh avoided any mention of the North's nuclear dispute in his speech.
Also Wednesday, more than 20,000 South Koreans, mostly Christians and war veterans, held a protest rally against Kim Jong-il, the North's leader, and his country's nuclear weapons programme.