High waves have hampered efforts to reach the ship
South Korea's President Lee Myung-bak has said there must be "no suspicion or negligence" in the probe into what sank a warship off the coast last week.
Rescue teams are still searching for 46 missing sailors but have detected no signs of life inside the ship.
Search efforts have been suspended for a second time, due to poor weather conditions and high waves.
US ships are involved in the operation and President Barack Obama has offered to send further help if needed.
The 1,200-tonne corvette, the Cheonan, sank after an explosion on Friday near Baengnyeong Island, close to the border with North Korea.
Seoul has said it is not clear what caused the explosion and has stressed there is no indication of North Korean involvement, although the defence minister has said a mine could be to blame.
Mr Lee said the issue was "a very sensitive and important question", Yonhap news agency reported.
He said Seoul would "find the cause through a thorough and scientific investigation" and that there should be "no suspicion or negligence" in the investigation.
"That is the way for South Korea to gain trust in the international community," he said.
In a telephone conversation to Mr Lee on Thursday, Mr Obama offered his condolences and said the US would offer more assistance if needed.
More than a dozen South Korean ships and a US vessel are involved in the rescue effort, but the operation was suspended for a second day on Thursday due to poor conditions.
Defence ministry spokesman Won Tae-jae said the ship was lying in relatively shallow water so was more affected by high seas.
"Since this morning's weather is bad, we are focusing on searching for the missing
Rescue divers have reached the part of the ship where the missing sailors could be, but heard no response when they tapped on the hull on Monday.
On Tuesday, one rescue diver died after losing consciousness as he searched the wreckage.
Mr Won also dismissed speculation that a North Korean submarine could have torpedoed the ship, saying no "extraordinary activities" had been confirmed.
"Let me be clear about this again, there were no activities which can be directly related to the accident," he said.
Because the search is taking place so close to the border with the North, Mr Lee has placed the military on alert.
Government officials have also been told not to take leave until tensions ease.
Military officials have said establishing a definitive cause might have to wait until the ship is salvaged.
Defence Minister Kim Tae-Young has said that the explosion could have been caused by a mine laid by the North during the 1950-53 Korean War - or intentionally sent floating towards the South Korean vessel by the communist state.
The Navy's chief of staff, Kim Sung-Chan, has said the ship's ammunition storage room did not appear to have exploded and "the ship was broken in two because of powerful outside pressure or an (exterior) explosion", AFP news agency reported.
Pyongyang has made no official comment on the incident.
It does not accept the maritime border, known as the Northern Limit Line, which was drawn unilaterally by the US-led United Nations Command at the end of the Korean War.
The sea border has been the scene of deadly clashes between the navies of the two Koreas in the past.