Search crews hoisted the tail of AirAsia Flight 8501 from the Java Sea on Saturday but the black boxes were not found inside.
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The black boxes, which feature cockpit voice and flight data recordings, may have dislodged from the plane's tail when it crashed into the sea on Dec. 28, Indonesian military commander Gen. Moeldoko told The Associated Press.
While the black boxes remain missing, ping-like sounds have been detected from the seabed, said Moeldoko.
"I am fully confident that the black boxes are still not far from the tail," he told The AP.
The discovery of the plane's tail earlier this week was a major breakthrough in the slow-moving search that has been hampered by seasonal rains, choppy seas, and blinding silt from river runoff.
At this point, nearly 50 bodies have been recovered from the crash, which killed 162 people.
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The Associated Press contributed to this report.