The recorders were originally examined in South Korea, the ministry said.
When the data was found to be missing, they were taken to the US and analysed by American safety regulators.
The plane was travelling from Bangkok on 29 December when it crash-landed at Muan International Airport and slid into a wall off the end of the runway, bursting into flames.
Sim Jai-dong, a former transport ministry accident investigator, told Reuters news agency that the loss of data from the crucial final minutes was surprising and suggested that all power, including back-up, could have been cut.
Many questions remain unanswered. Investigators have been looking at the role that a bird strike or weather conditions may have played.
They have also focused on why the Boeing 737-800 did not have its landing gear down when it hit the runway.
BBC News
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