His comments came a day after salvage workers raised the stern of the sunken ship from the sea bed, retrieving 38 bodies.
The remaining two-thirds of the ship, which was torn in two by the explosion, is expected to be raised next week.
The news is likely to fuel speculation of North Korean involvement in the sinking, possibly from a torpedo or mine, although South Korean officials have cautioned against jumping to conclusions.
One possibility is that it may have hit a mine left over from the 1950-53 Korean War.
Yoon said further analysis and time were needed to determine the exact cause of the blast, after salvaging the ship's other wreckage and collecting debris.
He also said the explosion may have occurred near the ship or that something may have hit the ship.
One former South Korean submarine captain, writing in South Korea's JoongAng Ilbo newspaper, said that judging by the damage to the ship the most likely cause of the sinking was a torpedo or mine.
"The Cheonan was halved in the middle," Jung Sung wrote.
"Therefore, it is highly likely that a torpedo fired from a submarine or mine destroyed the ship."
South Korean naval officials have said the Cheonan was on a routine patrol near the tense sea border with North Korea when it sank.
North Korea has made no comment on the incident.