A mini-sub hunting for Malaysian jet MH370 aborted its first search of the remote Indian Ocean seabed after just six hours because the water was deeper than its operating limits, officials said Tuesday.

The unmanned submarine loaded with sonar to map the ocean floor deployed Monday night from the Australian ship Ocean Shield which has spearheaded the hunt for the Boeing 777 that vanished on March 8.

"After completing around six hours of its mission, Bluefin-21 exceeded its operating depth limit of 4,500 metres and its built in safety feature returned it to the surface," JACC said, without detailing the exact depth of operations.

"The six hours of data gathered by the Autonomous Underwater Vehicle is currently being extracted and analysed," JACC said.

The AUV had been due to spend up to 16 hours collecting data.

US Navy Captain Mark Matthews explained the vehicle had exceeded its programmed operational limit and automatically resurfaced.

"There's certain abort criteria that the vehicle has as it's executing its mission," he told CNN from Perth.

"If there's certain conditions that occur, it stops and it comes to the surface.

"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."

Charts put the depth at 4,200-4,400 metres, he said.

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

Matthews, a search and recovery expert, said the crew would now refine the task to cope with the depth encountered.

"It happend in the very far corner of the area it's searching. So they are just shifting the search box a little bit away from that deep water."

The US-made Autonomous Underwater Vehicle (AUV) Bluefin-21 would embark on a second mission during the day, weather permitting, Australia's Joint Agency Coordination Centre (JACC) said.