A mine placed by North Korea during the Korean War may also have struck the ship, he said.
Many of the 3,000 Soviet-made mines North Korea planted during the war were removed, but not all. Kim said a North Korean mine was discovered as recently as 1984.
Kim also ruled out a torpedo attack and officials said an internal malfunction may be to blame for the explosion.
North Korea's state media has made no mention of the ship. The country's first comments since the ship went down warned the US and South Korea on Monday against engaging in "psychological warfare" by letting journalists into the demilitarised zone.
Fifty-eight crew members were rescued from the Yellow Sea waters near Baengnyeong Island west of Seoul, but 46 others are still missing.
On Monday South Korean officials said there was no information on the fate of the missing crew.
"We plan to do the rescue work in the belief that there could be still survivors both in the stern and the bow," Lee Ki-Shik, the spokesman for the Joint Chiefs of Staff, told a news briefing.
"The rapid currents and poor visibility under the sea are the biggest stumbling block."
The families of the missing have demanded swifter rescue efforts amid growing anger after divers postponed earlier attempts to reach the stern due to strong currents, poor visibility and high waves.
But the prospect of pulling out anyone alive seemed dim. Any navy crewmen who initially survived and managed to seal themselves inside watertight cabins would likely have run out of air by Monday night since the supply of oxygen in the cabins was estimated to last up to 69 hours.
The disputed sea border with North Korea was the scene of deadly naval clashes in 1999 and 2002 and of a firefight last November.
North Korea refuses to accept the maritime border known as the Northern Limit Line, which was drawn up by UN forces after the 1950-53 Korean war.
It says the line should run further to the south.
In January, the North fired 370 artillery shells into the sea near the border, raising tensions between the two countries.