Azharuddin Abdul Rahman, director-general of the Department of Civil Aviation, said the plane returned to Kuala Lumpur International Airport because it was unable to maintain the correct pressure inside the aircraft.
"It was not able to maintain the right pressure differential for the comfort of the passengers. It is not a major problem," he said.
Malaysia Airlines officials could not be reached for comment.
Meanwhile the Star Online reported that the Tokyo-bound flight was 50 minutes into its journey when it was forced to return to Kuala Lumpur after taking off at 0250 GMT (9.50am Thailand time).
Passengers were subsequently transferred to another plane which departed at 0515 GMT, it said.
The flag carrier, which prior to this year had a good safety record, has been in the spotlight in the past six months following two aviation tragedies -- the disappearance of flight MH370 on March 8, and the shooting down of MH17 on July 17 while flying over rebel-held eastern Ukraine.
The two aviation tragedies killed 537 passengers.