Australian air force AP-3C Orion aircraft detected the signal in the area where an Australian vessel picked up pings earlier this week.
Authorities say the acoustic data shows potential of being from a man-made source.
The data is now under analysis.
If confirmed, the signal can further narrow the hunt for the missing jetliner, which vanished early in March while flying from Kuala Lumpur to Beijing with 239 people aboard.
Thursday's search was confined to just under 58,000 square kilometers in the southern Indian Ocean.
Narrowing the search area is crucial before an unmanned submarine can be sent to create a sonar map of a potential debris field on the seabed.
William O'Halloran is the Director of Marine Operations at Bluefin Robotics, which manufactured the submarine.
"One of the great things about it is that it can work at the extreme operational environment, at the great depths that we're expected to have to survey. And that allows us to put the vehicle down, map the area and return objects of interest."
O'Halloran says since the sub moves slowly, it will take six-to-eight weeks to canvass the current underwater search zone, which is a 1,300 square kilometer patch on the ocean floor.
The Australia air force has been dropping sonar buoys to maximize the sound-detectors operating in the search zone.
Up to 14 planes and 13 ships have been assigned to assist in Thursday's search.
The Chinese Foreign Ministry says China will spare no efforts in the search as it is now a critical stage to locate the black boxes.
Nine Chinese vessels have joined the search.
Meanwhile, as the investigation of the flight crew continues, it is reported that the flight's captain was the last person on the jet to speak to air-traffic controllers.
Previously, media reports suggested the final words had been spoken by the co-pilot.
It is said that there is nothing unusual about the captain's voice and there were no third-party voices.
For CRI, I am Yu Yang.
