Cho Byung Jae said a South Korean navy warship was heading toward the vessel, the Yonhap News Agency reported.
The company that owns the Hanjin Tianjin container ship lost contact with it Thursday when it was about 850 kilometres off the coast of Somalia.
Pirates reportedly attacked and captured the ship while it was sailing from Spain to Singapore.
'It's a very fluid and sensitive situation,' presidential spokesman Hong Sang Pyo said, declining to give details of the navy ship's plans.
A South Korean anti-piracy unit operates off Somalia.
South Korea's Hanjin Shipping Co owns the 75,000-ton vessel, which is registered in Panama.
The crew consisted of 14 South Koreans and six Indonesians.