The break in the search for Sriwijaya Air Flight 182 came after sonar equipment on a navy ship detected a signal from the aircraft at a location that fit the coordinates from the last contact made by the pilots before the plane went missing on Saturday afternoon.
It's still unclear what caused the crash. There was no sign of survivors.
"I represent the government and all Indonesians in expressing my deep condolences for this tragedy," President Joko Widodo said.
"We are doing our best to save the victims. We pray together so that the victims can be found," he said, adding that he had asked the National Transport Safety Committee to conduct an investigation.
Fishermen in the area between Lancang and Laki islands, part of an archipelago around Thousand Islands north of Jakarta's coast, reported hearing an explosion around 2:30 p.m. Saturday.
"We heard something explode, we thought it was a bomb or a tsunami since after that we saw the big splash from the water," Solihin, who goes by one name, told The Associated Press by phone.
"It was raining heavily and the weather was so bad. So it is difficult to see around clearly. But we can see the splash and a big wave after the sounds. We were very shocked and directly saw the plane debris and the fuel around our boat."
Transportation Minister Budi Karya Sumadi said Flight SJ182 was delayed for an hour before it took off at 2:36 p.m. It disappeared from radar four minutes later, after the pilot contacted air traffic control to ascend to an altitude of 8,839m, he said.
There were 62 people on board, including seven children and three babies.
"We are aware of media reports from Jakarta regarding Sriwijaya Air flight SJ-182," Boeing said in a statement. "Our thoughts are with the crew, passengers, and their families. We are in contact with our airline customer and stand ready to support them during this difficult time."
Authorities established two crisis centers, one at airport and one at port. Families gathered to wait for news of loved ones.
On social media, people began circulating the flight manifesto with photos and videos of those who were listed as passengers. One video shows a woman with her children waving goodbye while walking through the airport.
- AP