"For now, we don't see errors on the part of the team, we are asking questions regarding part of the system that controls the landing," said Nikolai Zelenshchikov, number two at RKK Energiya, which builds Soyuz spacecraft.
A Russian team looking into the landing is due to inform US space agency NASA of its results this week, he added, quoted by ITAR-TASS news agency.
No US experts had been invited to sit on the investigating team, whose final report is due to be delivered on May 23.
The US-Russian trio made an uncontrolled entry on May 4, landing nearly 500 kilometers (310 miles) off target in the plains of Kazakhstan after an apparent computer malfunction on board forced them to abort the automatic landing.
Initial reports said the steeper than expected entry occured after US astronauts Kenneth Bowersox and Donald Pettit and Russian cosmonaut Nikolai Budarin pressed the wrong button.
The flight from the International Space Station (ISS) marked the first landing on a Russian-made Soyuz TMA-1 craft since the United States grounded its space fleet in the wake of the Columbia space shuttle disaster on Febraury
A team of Russian experts is also due to examine the rest of the modified spacecraft in the Soyuz series, Zelenshchikov said.
One Soyuz is currently docked at the ISS and another is due to blast off for the rotating space station later in the year.
Columbia disintegrated during re-entry to the Earth's atmosphere, killing all seven crew members and leading NASA to suspend all shuttle missions, including those to the ISS.
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