Russia's Interfax news agency quoted an unidentified official as saying that the capsule entered the atmosphere hatch-first instead of with its heat shields leading the way.
The official, who is reportedly involved in an investigation into the landing, said improper alignment caused significant damage to the hatch and part of a key valve that equalizes pressure inside and outside the capsule.
As a result, Yi, Peggy Whitson, a US astronaut and Yuri Malenchenko, a Russian flight engineer, endured severe gravitational forces after the space craft took a steeper-than-usual re-entry known as a "ballistic trajectory".
"The fact that the entire crew ended up whole and undamaged is a great success. Everything could have turned out much worse," Interfax quoted the official as saying.
Spacecraft based on 1960s technology, first manned flight in 1967
Designed by legendary Soviet chief space designer, Sergei Korolev
Regarded as the workhorse of Russia's manned space programme
One Soyuz spacecraft is always docked to space station as emergency escape "lifeboat"
After retirement of space shuttle in 2010, Soyuz will become sole means of transporting crews to space station
"You could say the situation was on a razor's edge."
The incident was the second time in a row – and the third since 2003 - that a Soyuz landing had gone awry.
The official quoted by Interfax said the TMA-11 capsule's antenna burned up during the descent, interrupting communications with Russian Mission Control.
The crew was returning from a six-month mission aboard the International Space Station (ISS).
The official quoted by Interfax also said the incident showed there were problems with the Russian space programme.
"Considering that this situation has repeated itself, it is obvious that the technological discipline in preparing space equipment for a flight is declining," the official was quoted as saying.
"There is no guarantee that the crew of a Soyuz spacecraft landing a half a year from now would not face the same difficulties."
US and Russian space agency officials however played down the incident including the time taken to re-establish communications with ground control to confirm a safe landing.
Alexander Vorobyov, a spokesman for the Russian Federal Space Agency, confirmed there were problems during the descent but said the resulting damage was a common occurrence during re-entry.
Following the incident, the US space agency said it was confident Russia's Soyuz capsules were still safe to use.
"There is no immediate implication to the Soyuz vehicle on orbit," William Gerstenmaier, an associate administrator for Nasa's space operations, said.
"If we need to return for an emergency case, we can get in the Soyuz and come home."
Crew aboard the ISS rely on a Soyuz spacecraft that is permanently attached to the station for use as a space lifeboat in case of an emergency.
|Russian officials are investigating why the|
capsule landed off target [Reuters]
Russia's Soyuz spacecraft will also become the sole means of delivering and returning crew from the space station after Nasa's ageing fleet of space shuttles are retired from service in 2010
Gerstenmaier said Nasa was not aware of any danger to the crew and did not see it as a major problem.
But, he added, "it's clearly something that should not have occurred."
Expressing "complete confidence" in Russia's handling of the mishap, he said there was no need to overreact to the incident.
Gerstenmaier said Malenchenko "detected some smoke in the cabin" and managed to get out of the capsule by himself, while Whitson and Yi received help from locals.
On Tuesday Nasa released an audio recording in which Whitson described parts of the return as "a little more dramatic than I was expecting".
"It wasn't the search and rescue who got us out of the capsule," Whitson said.
"It was just some guys that had seen it and drove in. They probably saw the fire and drove in toward the scene."