Autonomous underwater vehicle Bluefin 21, a US Navy probe equipped with side-scan sonar, was deployed last month from the Australian navy ship Ocean Shield to map the ocean floor.
The Beijing-bound Malaysia Airlines flight MH370 - carrying 239 people, including five Indians, an Indo-Canadian and 154 Chinese nationals - had mysteriously vanished on March 8 after taking off from Kuala Lumpur.
No wreckage of the Malaysian Airlines Flight MH370 has been found, despite a massive international search operation.
The Bluefin-21 and the transponder were damaged this week when the vehicle was being hoisted onto the deck of the ship. The vehicle struck the navigation transponder, which extends over the side of the ship, US Navy's deputy director of ocean engineering Michael Dean was quoted as saying by CNN.
Repairs were made to the submersible. But in subsequent tests, operators said the acoustic communications link on the Bluefin-21 and the navigation transponder on the Ocean Shield malfunctioned.
No spare parts for either device were on the ship, Dean said, adding that parts necessary for the repairs are being shipped from the United Kingdom to Australia.
Dean earlier said that it will take four or five days to get parts to the ship. But it could take longer if the Ocean Shield has to return to port.
The robotic submarine had conducted about 18 missions in the southern Indian Ocean before the Ocean Shield returned to port to refuel. But the submersible has been bedeviled with problems since returning to the search site this week.
Shortly after the submersible was placed in the water, Dean said, operators had trouble communicating with it, and they decided to retrieve it. But while they hoisted the Bluefin in 20-knot winds and 3- to 5-foot seas, the Bluefin struck the side of the Ocean Shield and hit the transponder.
Australia's Joint Agency Coordination Agency (JACC) blamed "communications problems" for the aborted mission.
"Examination of the communications problem has established that a hardware defect exists in the transponder mounted on the Ocean Shield and a defect may also exist in the transponder mounted on the Bluefin-21," JACC said.
The mystery of the missing plane continued to baffle aviation and security authorities who have so far not succeeded in tracking the aircraft despite deploying hi-tech radar and other gadgets.