A defense ministry official said the unidentified object the vessel had fired at on Friday night near the western sea border that divides the two Koreas may well have been a flock of birds.
Initial speculation that North Korea might be to blame caused ripples on Wall Street, where share prices dipped partly on geopolitical concerns, and the South Korean won dropped against the dollar.
"It is premature at this stage to discuss the cause of the sinking," presidential spokeswoman Kim Eun-hye said after an early Saturday morning government meeting.
"It has not been determined whether this incident is related to North Korea."
The Joint Chiefs of Staff also said it could not conclude that the reclusive North was behind the attack.
Local media quoted a presidential official as saying satellite pictures and other information showed no sign of the North Korean military in the area at the time of the sinking.
The defense ministry said 58 of the 104 on board had been rescued and Yonhap quoted navy officials as saying several had died. It was later quoted as saying 46 were still missing.
"An unidentified reason caused a hole in the ship, which led to its sinking. Currently 58 have been rescued out of the total 104 on board. Rescue efforts are under way," the ministry said.
"The ship fired a warning shot at an unidentified object, and the object was later suspected to have been a flock of birds. But we are checking."
Earlier, South Korean media had quoted officials as saying the North could have torpedoed the ship. One said it could have struck a mine near what is one of the world's most heavily militarized borders.
"The loud firing sound remained for about 15 minutes, while I watched TV. I never heard such loud firing sound in my entire life staying at Back-ryung island, and the sound was definitely different from those heard from usual drills," Yonhap news agency quoted one 56-year-old resident on a nearby island as saying.
COLD SHOULDER
The sinking occurred as the impoverished North has grown increasingly frustrated by its wealthy neighbor, which has given the cold-shoulder to recent attempts to reopen a lucrative tourist business on the northern side of the frontier.
It also coincides with mounting pressure on Pyongyang to end a more than one-year boycott of international talks to end its efforts to build a nuclear arsenal.
Reports of a possible naval clash saw the won weaken roughly 0.45 percent against the dollar and were cited by analysts as one reason for a dip in U.S. stocks.
The price to insure Korean sovereign debt rose to 83 basis points from 78 basis points in the wake of the news, according to two trading sources. That means the cost to insure $10 million in South Korean debt increased by $5,000 to $83,000.
Markets have become largely inured to saber-rattling by North Korea but it has in the past caused brief jitters.
The ship sank near the disputed Yellow Sea border off the west coast of the peninsula which was the scene of two deadly naval fights between the rival Koreas in the past decade.
Navies from the rival Koreas exchanged gunfire for the first time in seven years in the Yellow Sea waters in November, damaging vessels on both sides.
The West has been pressuring North Korea to give up efforts to build nuclear weapons, promising help for its broken economy if it does so.
There has been widespread speculation that North Korea's ruler, Kim Jong-il, was about to visit China, his only significant ally and on which he has depended almost entirely for economic aid after a new conservative government in Seoul effectively ended years of free-flowing assistance.
(Additional reporting by Cheon Jong-woo, Kim Miyoung, Jon Herskovitz and Jonathan Thatcher; Writing by Jonathan Thatcher)