The admission is likely to add to criticism of the Malaysian authorities’ handling of the search for the Malaysia Airlines flight which vanished on March 8 during a flight from Kuala Lumpur to Beijing.
Chinese relatives of those on board the missing plane have been particularly scathing, accusing Malaysia of incompetence and even a cover-up.
“We would like to confirm that the last conversation in the transcript between the air traffic controller and the cockpit is at 0119 (Malaysian time) and is ‘Good night Malaysian three seven zero’,” the department said in a statement on Monday night.
“The authorities are still doing forensic investigation to determine whether those last words from the cockpit were by the pilot or the co-pilot.”
Malaysia Airlines CEO Ahmad Jauhari Yahya had said on March 17 the last words from the cockpit were believed to have been spoken by the co-pilot.
Shortly after the last message from the plane communications were cut and the Boeing 777, carrying mostly Chinese nationals, vanished from civilian radar.
The civil aviation department said a full transcript would be released during a briefing with relatives of the missing passengers.
The move comes after testy exchanges on Monday between foreign journalists and Malaysian Transport and Defence Minister Hishammuddin Hussein, who insisted: “We are not hiding anything, we are just following the procedure that has been set.”