A mini-sub searching for missing Flight MH370 was again sweeping the Indian Ocean seabed Wednesday after drawing a blank on a first mission aborted at daunting depths in a laborious operation that could take months.

The unmanned submarine equipped with sonar gear was deployed Tuesday night after data analysis of the first failed foray produced nothing of interest, Australia's Joint Agency Coordination Centre said.

After more than three weeks of hunting for black box signals, the autonomous sub had been deployed for the first time on Monday night from the Australian ship Ocean Shield, which has spearheaded the hunt for the Boeing 777 that vanished on March 8 with 239 people aboard.

"The autonomous underwater vehicle was again deployed last night (Tuesday) from ADV (Australian Defence Vessel) Ocean Shield," JACC said.

"The data from Bluefin-21's first mission has been downloaded and analysed. No objects of interest were found," JACC said.

The US navy explained that the Bluefin-21 had automatically aborted after six hours upon breaching its maximum operating depth.

JACC added that it had "exceeded its operating depth limit of 4,500 metres (15,000 feet) and its built-in safety feature returned it to the surface".

The sub was undamaged and had to be re-programmed, said US Navy Captain Mark Matthews.

"In this case the vehicle's programmed to fly 30 metres over the floor of the ocean to get a good mapping of what's beneath," he told CNN from Perth after the aborted dive.

"It went to 4,500 metres and once it hit that max depth, it said 'This is deeper than I'm programmed to be', so it aborted the mission."

'Two months to scan area'

Questions were raised about how deep the seabed may be in the search area.

JACC chief Angus Houston has stressed that the AUV cannot operate below 4,500 metres and that other vehicles would have to be brought in to cope with greater depths.

"There are vehicles that can go a lot deeper than that," he said Monday. "They are usually much larger vehicles; they do recovery as well and obviously those sorts of possibilities will be looked at ... They are being looked at as we speak.

"But a lot will depend on the outcome of what we find when we go down and take a look," said Houston who has not revealed what has been seen so far.

He had announced Monday the end of listening for signals from the plane's black boxes and launch of the submarine operation.

The mini-sub is supposed to conduct a sonar survey of the silty ocean floor for 16 hours at a time looking for wreckage from the Malaysia Airlines flight which disappeared en route from Kuala Lumpur to Beijing.

The US Navy estimated it would take the Bluefin-21 "anywhere from six weeks to two months to scan the entire search area", which has been narrowed using satellite data and the detection of electronic pulses linked to black box recorders which were last heard more than a week ago.

Houston has described the detections as the best lead in the hunt for the plane, and added Monday that an oil slick had also been sighted in the search area.

It would take several days to test a sample of the oil ashore, but Houston said he did not think it was from one of the many ships involved in the hunt.

The cause of the plane's disappearance, after being diverted hundreds of kilometres (miles) off course, remains a mystery. No debris has been found despite an enormous search involving ships and planes from several nations.

If the black boxes are found, Malaysia's Transport Minister Hishammuddin Hussein pledged Tuesday to make public any data recovered, as the government battles widespread criticism over the transparency of its investigation.

The Malaysian government has been tight-lipped about its ongoing investigation into the disappearance of the jet, adding to the anger and frustration of relatives.