The way U.S. officials see it, there’s little mystery behind the most notorious shipwreck in recent Korean history.

Secretary of State Hillary Rodham Clinton calls the evidence “overwhelming” that the Cheonan, a South Korean warship that sank in March, was hit by a North Korean torpedo. Vice President Joe Biden has cited the South Korean-led panel investigating the sinking as a model of transparency.

But challenges to the official version of events are coming from an unlikely place: within South Korea.

Armed with dossiers of their own scientific studies and bolstered by conspiracy theories, critics dispute the findings announced May 20 by South Korean President Lee Myung-bak, which pointed a finger at Pyongyang.

They also question why Lee made the announcement nearly two months after the ship’s sinking, on the very day campaigning opened for fiercely contested local elections. Many accuse the conservative leader of using the deaths of 46 sailors to stir up anti-communist sentiment and sway the vote.

The critics, mostly but not all from the opposition, say it is unlikely that the impoverished North Korean regime could have pulled off a perfectly executed hit against a superior military power, sneaking a submarine into the area and slipping away without detection. They also wonder whether the evidence of a torpedo attack was misinterpreted, or even fabricated.

“I couldn’t find the slightest sign of an explosion,” said Shin Sang-chul, a former shipbuilding executive-turned-investigative journalist. “The sailors drowned to death. Their bodies were clean. We didn’t even find dead fish in the sea.”

Shin, who was appointed to the joint investigative panel by the opposition Democratic Party, inspected the damaged ship with other experts April 30. He was removed from the panel shortly afterward, he says, because he had voiced a contrary opinion: that the Cheonan hit ground in the shallow water off the Korean peninsula and then damaged its hull trying to get off a reef.

“It was the equivalent of a simple traffic accident at sea,” Shin said.

The Defense Ministry said in a statement that Shin was removed because of “limited expertise, a lack of objectivity and scientific logic,” and that he was “intentionally creating public mistrust” in the investigation.

The doubts about the Cheonan have embarrassed the United States, which will s begin joint military exercises Sunday in a show of unity against North Korean aggression. On Friday, an angry North Korea warned that “there will be a physical response” to the maneuvers.

Two South Korean-born U.S. academics have joined the chorus of skepticism, holding a news conference this month in Tokyo to voice their suspicions about the “smoking gun:” a piece of torpedo propeller with a handwritten mark in blue ink reading “No. 1" in Korean.

“You could put that mark on an iPhone and claim it was manufactured in North Korea,” scoffed one of the academics, Seunghun Lee, a professor of physics at the University of Virginia.

Lee called the discovery of the propeller fragment five days before the government’s news conference suspicious. The salvaged part had more corrosion than would have been expected after just 50 days in the water, yet the blue writing was surprisingly clear, he said.

“The government is lying when they said this was found underwater. I think this is something that was pulled out of a warehouse of old materials to show to the press,” Lee said.

South Korean politicians say they’ve been left in the dark about the investigation.

“We asked for very basic information: interviews with surviving sailors, communication records, the reason the ship was out there,” said Choi Moon-soon, an assemblyman with the Democratic Party.

The legislature also has not been allowed to see the full report by the investigative committee, only a five-page synopsis.

“I don’t know why they haven’t released the report. They are trying to cover up small inconsistencies, and that has cost them credibility,” said Kim Chul-woo, a former Defense Ministry official who is now an analyst with the Korea Institute for Defense Analyses, a government think tank.

A military oversight body, the Board of Inspection and Audit, has accused senior naval officers of lying and concealing information.

“Military officers deliberately left out or distorted key information in their report to senior officials and the public because they wanted to avoid being held to account for being unprepared,” an official of the inspection board was quoted as telling the South Korean newspaper Chosun Ilbo.

The Cheonan, a 1,200-ton corvette, sank the night of March 26 about 12 miles off North Korea. The first report issued by Yonhap, the official South Korean news agency, said the ship had been struck by a torpedo, but soon afterward the story changed to say the ship sank after being grounded on a reef.

The military repeated that version for days. The audit board found that sailors on a nearby vessel, the Sokcho, who fired off 35 shots with a 76-millimeter cannon around the time of the sinking, were instructed to say they’d been shooting at a flock of birds, even though at first they had said they’d seen a suspected submarine on radar.

On April 2, as Defense Minister Kim Tae-young was testifying before the National Assembly, a cameraman shooting over his right shoulder managed to capture an image of a handwritten note from the president’s office instructing him not to talk about North Korean submarines.

Such inconsistencies and reversals have fueled the suspicions of government critics. U.S. officials, however, say the panel’s conclusion is irrefutable.

Rear Adm. Thomas J. Eccles, the senior U.S. representative on the panel, said investigators considered all possibilities: a grounding, an internal explosion, a collision with a mine. But they quickly concluded that the boat was sunk by a bubble-jet torpedo, which exploded underneath the vessel and didn’t leave the usual signs of an explosion, he said.

“The pattern of damage was exactly aligned with that kind of weapon,” Eccles said in a telephone interview. “Torpedoes these days are designed to drive underneath the target and explode. They use the energy of their explosion to make a bubble that expands and contracts. It is designed to break the back of the ship.”

Pyongyang, meanwhile, denies involvement in the sinking and calls the accusation against it a fabrication.

South Koreans themselves appear to be confused: Polls show that more than 20% of the public doesn’t believe North Korea sank the Cheonan.

Wi Sung-lac, South Korea’s top envoy for North Korean affairs, says the criticism from within has made it difficult to get China and Russia on board to punish Pyongyang for the attack.

“They say, ‘But even in your own country, many people don’t believe the result,’ ” Wi said.

barbara.demick@latimes.com

john.glionna@latimes.com

Ju-min Park of The Times’ Seoul Bureau and David S. Cloud of the Washington bureau contributed to this report.