Authorities investigating the disaster - the worst on South Korean soil - that killed 179 people plan to analyse what caused the black boxes to stop recording, the ministry said in a statement on Saturday.
The voice recorder was initially analysed in South Korea.
The disaster, which killed 179 people and injured two, was the worst on South Korean soil. (AP PHOTO)
When data was found to be missing, it was sent to a US National Transportation Safety Board laboratory, the ministry said.
The damaged flight data recorder was taken to the US for analysis in co-operation with the US safety regulator, the ministry has said.
Jeju Air 7C2216, which departed the Thai capital Bangkok for Muan in southwest South Korea, belly-landed and overshot the regional airport's runway, exploding into flames after hitting an embankment.
The pilots told air traffic control the aircraft had suffered a bird strike and declared an emergency about four minutes before it crashed into the embankment, exploding in flames.Â
Two injured crew members, sitting in the tail section, were rescued.
Two minutes before the Mayday emergency call, air traffic control gave caution for "bird activity".
The pilots told air traffic control the aircraft had suffered a bird strike. (AP PHOTO)
Declaring an emergency, the pilots abandoned the landing attempt and initiated a go-around.
But instead of making a full go-about, the budget airline's Boeing 737-800 jet took a sharp turn and approached the airport's single runway from the opposite end, crash-landing without landing gear deployed.
Sim Jai-dong, a former transport ministry accident investigator, said the discovery of the missing data from the crucial final minutes was surprising and suggested all power including backup might have been cut, which was rare.
The transport ministry said other data available would be used in the investigation and that it would ensure the probe was transparent and that information was shared with the victims' families.
Some members of the victims' families have said the transport ministry should not be taking the lead in the investigation but that it should involve independent experts including those recommended by the families.
The investigation of the crash has also focused on the embankment, which was designed to prop up the "localiser" system used to assist aircraft landing, including why it was built with such rigid material and so close to the end of the runway.
