The flight recorder, retrieved from the wreckage at Muan International Airport, was damaged and missing a connector that links its data storage unit to the power supply.
Joo Jong-wan, director of the aviation policy division at the ministry, said: "We have determined that extracting data from the damaged flight data recorder here is not possible.
Watch haunting moment mourning South Korea marks New Year with SILENT crowds after plane disaster and ‘coup’ drama
"And so we have agreed with the NTSB to send it to the US and analyze it there."
A team from the US is also investigating on site at Muan airport with South Korean officials.
Investigators are focusing on a navigation system that assists in aircraft landings, known as a localiser.
The localiser, installed on a concrete structure, has been widely blamed for the high number of casualties.
The jet was approaching the airport when its right engine was struck - which could have forced the pilot to shut down the damaged engine.
Several attempts to land were aborted by the pilot before a final decision was made to attempt it.
The aircraft quickly hit the tarmac - but the pilot's heroic landing was all done in vain as it continued to speed off the end of the runway.
Seconds later it smashed into a concrete wall at the end of the 2,800-metre runway.
7
Family members of a victim of the Jeju Air plane crash grieve at a temporary shelter at Muan International AirportCredit: EPA
7
A mourner pays her respects at a memorial altarCredit: AFP
7
A police forensics team conducts an investigation at the sceneCredit: AFP
The plane instantly exploded after hitting the structure.
Officials have said investigators are examining whether a bird strike, a failure of the landing gear to drop or if problems with any other control systems played a role in the disaster.
They will also investigate the pilot's apparent rush to attempt a landing right after he had declared an emergency, officials have said.
Two crew members, located near the tail of the Boeing 737-800, survived.
Air safety experts have questioned if the airport embankment designed to prop up navigation equipment was built too close to the end of the runway.
7
South Korea's acting President Choi Sang-mok on Wednesday called for a fair and objective investigation, and said funeral procedures have begun after all the victims were formally identified.
He said: "The most urgent matter at present is to return the victims to their families."
Airport authorities set up an altar late on Tuesday, and on Wednesday buses carried relatives of victims to the crash site so that they could pay their respects.
The Muan airport was brimming with mourners seeking to pay their tributes at the altar, leading to a queue of several hundred metres.
Park Han-shin, who has been liasing with airport and government authorities on behalf of the bereaved families, said that almost 700 family members visited the crash site.
Park also added there was a list of 43 bodies ready to be released, asking relatives of those not on the list for patience.
