It was the fifth attempt by the Bluefin-21 unmanned sub to find wreckage or the black boxes from Flight 370 in a distant patch of seabed off Australia's west coast.
The sub has covered 42 square miles of the sea bed, but has found nothing.
Officials are desperate to find some physical evidence that they are searching in the right spot for the Boeing 777, which vanished on March 8 with 239 on board on a flight from Kuala Lumpur, Malaysia, to Beijing.
A weeks-long search of the ocean surface has not turned up a single piece of debris, and officials have determined that an oil slick found in the search zone did not come from the plane.
The Bluefin is searching a remote stretch of ocean floor about 15,000ft deep in an area where sound-locating equipment picked up a series of underwater sounds consistent with a plane's black box.
Australian prime minister Tony Abbott has said officials are "very confident" the sounds came from the Malaysian jet's cockpit voice and flight data recorders, but finding the devices in such deep water is an incredibly difficult task.
Radar and satellite data show the plane flew far off course and would have run out of fuel in a remote section of the Indian Ocean.
Eleven planes and 12 ships are continuing the surface search across a 20,000- square-mile patch of ocean.
Angus Houston, who is heading the search effort, said earlier this week that the hunt for floating debris would be ending within days because it is unlikely anything will be found. But the search co-ordination centre said the effort would continue into next week.
Malaysia's defence minister, Hishamuddin Hussein, confirmed the search would continue through the Easter weekend, but acknowledged that officials would have to rethink their strategy if nothing is found.
The US Navy's unmanned sub cut short its mission on Monday as it exceeded its maximum depth of 15,000ft.