"We found the data recorder yesterday and our team at the site is now trying to retrieve its cockpit voice recorder (CVR) from below the sea," transport safety committee chairman Tatang Kurniadi told AFP.
The MA-60 turbo-prop plane operated by Merpati Nusantara, one of the Indonesian airlines banned from European airspace, crashed into the sea as it was attempting to land during a heavy downpour on Saturday, officials said.
It was flying from Sorong to Kaimana airport in West Papua province.
Data from the black box will be sent to laboratories in China for clues about why the plane crashed, Kurniadi said.
"The investigation is still ongoing. We need time to listen to the CVR and to analyse it," he said, adding that four investigators were still at the crash site.
Merpati spokesman Imam Turihi said it was too early to say why the plane crashed.
"We're now focusing on taking care of the victims' bodies, before they are sent to their families," he told AFP, adding that 22 bodies including two babies had been recovered.
He revised down the total number of people on board to 25, from 27 as initially reported, and confirmed that there were no foreigners among the passengers or crew.
In 2009, a Twin Otter plane also operated by Merpati Nusantara crashed into a mountain in remote Papua province, killing all 16 people on board.
Another of the airline's planes overran a runway after landing in Manokwari in West Papua in April last year, breaking into three pieces and injuring 44 of the more than 100 people on board.
The European Union banned all Indonesian airlines from entering its airspace in 2007, but relaxed the ban on some carriers two years later after it said safety issues had been resolved.
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