The Australian agency coordinating the search effort, now in its third month, said communications equipment on the sophisticated Bluefin-21 drone was damaged on its first day back after almost two weeks away for maintenance and resupply.
The issue was discovered on Wednesday, the Joint Agency Coordination Centre (JACC) said, just two hours into the drone's first mission since returning to the search area in the Indian Ocean about 1,600 km (1,000 miles) northwest of the west Australian city of Perth.
"Examination of the communications problem has established that a hardware defect exists in the transponder mounted on the Ocean Shield and that a defect may also exist in the transponder mounted on the Bluefin-21," a JACC statement said, referring to the Australian naval vessel towing the drone.
"This inhibits the ability of the two devices to communicate with each other," it said,
The Boeing 777 disappeared on March 8 along with its 239 passengers and crew during a scheduled service between Kuala Lumpur and Beijing, sparking the most expensive search in aviation history.
Aerial searches failed to turn up any sign of the plane and officials are now relying on unmanned submersibles like the Bluefin-21, which scour the ocean floor using sophisticated sonar equipment.
Officials have said that it could take a year to search the 60,000 sq km (23,000 sq mile) area where the plane is believed to have crashed, and questions about how to proceed and how to split the bill are growing.
Parts to repair the Bluefin drone, on loan from the U.S. Navy for less than three more weeks, will not arrive in Australia until Sunday and it will take several days to reach the search area once repairs are completed.