Busan, the world's fifth largest container port, handled a total 11.98 million TEU in 2009, down from 13.45 million in 2008, data from the Busan Port Authority (BPA) showed.
The figures were evidence of the impact of the global economic slowdown, analysts said.
Singapore, the world's busiest container port, handled 25.87 million TEU in 2009, 13.5% down from 29.92 million TEU the previous year.
The world's second busiest port, Shanghai, is estimated to have handled about 24 million TEU in 2009, down from 28 million TEU in 2008, according to Wang Hongquan, vice-director for the Shanghai Transport and Port Authority.