Images taken by a remote-controlled vehicle from the ship showed parts of the plane’s wing and words on the fuselage, Singapore defence minister Ng Eng Hen said on his Facebook page.
The AirAsia slogan “Now every-one can fly” could be seen on the wreckage in the pictures.
Indonesian search officials have been notified so they can begin recovery operations, he said.
The fuselage section that was found is 30 metres long and ten metres wide with a height of three metres, Indonesia’s National Search and Rescue Agency chief Henry Bambang Soelistyo said.
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“The fuselage with a wing still attached on it was found in the priority search area and has been confirmed as part of the AirAsia plane,” Mr Soelistyo said.
He added it was some 1.8 miles from the tail, which was found earlier, and 800 metres from the black boxes, at a depth of about 28 metres (92ft).
The plane carrying 162 people disappeared from radar on December 28 less than halfway into a two-hour flight from Surabaya, Indonesia, to Singapore. Many of the victims are believed to be entombed in the main section of the aircraft’s cabin.
Fishermen found two bodies along with plane seats and debris off the coast off South Kalimantan, bringing to 50 the total of bodies recovered so far.
President Joko Widodo expressed happiness at the discovery, saying that divers would examine the fuselage today.
The plane’s black boxes – the flight data recorder and cockpit flight recorder – were retrieved earlier this week and will be key to learning what caused the plane to crash. Bad weather is a suspected factor.
AirAsia lost contact with the flight on 28 December as it was flying from Surabaya in Indonesia to Singapore with 162 people on board.
Dozens of bodies have been found but many of the passengers and crew are thought to still be inside the plane, which made finding the fuselage so important.
The pilot of the AirAsia flight had asked for a route change because of stormy weather before contact was lost, but it is not yet known for certain what brought down the plane.
Mr Soelistyo, had said that what they suspected was the fuselage had been spotted by search teams on Tuesday but that they were waiting for confirmation.
He said it was not yet clear whether there were bodies inside, but that authorities hoped that was the case.
Earlier in the day, when the wreckage was being investigated by divers, the official co-ordinating the search, SB Supriyadi, said that raising the fuselage would be a tricky operation and authorities would have to determine the best course of action.
“If it is not too heavy, we may lift the whole piece and evacuate the victims,” said Mr Supriyadi.
“If it’s too heavy, we may then swim into the fuselage and pull out the bodies one by one before lifting it.”
Since the plane disappeared over the Java Sea between Christmas and New Year, a multi-national search has been under way involving aerial searches and more than 30 ships.
However, strong currents, high waves and poor visibility have slowed down search and rescue efforts. Most of those on board the flight were Indonesian nationals.