Herson, chief of the airport authority for the Bali-Nusa Tenggara area, told Reuters that after the call the pilot updated the control tower to say that the plane was flying normally and he would not return to the airport as requested.
"Every aircraft that we have will go through transit, pre-flight and post-flight checks", said Lion Air's Prihantoro.
Passengers on the Sunday flight from Bali to Jakarta have recounted problems that including a long-delayed take-off for an engine check and terrifying descents in the first 10 minutes in the air. They are a step down from Mayday, which signals severe distress.
Search teams have been scouring the seabed for the fuselage of the Boeing-737 MAX 8, which plunged into the waters off Indonesia's northern coast shortly after takeoff Monday despite only having been in service a few months.
The fatal flight's pilots also made a "return to base" request minutes before the crash.
While investigations are ongoing, there are a selfies clicked by the passengers just before their ill-fated flight that have emerged online.
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But according to the transport safety committee, the plane had technical problems on its previous flight on Sunday, from the city of Denpasar on the resort island of Bali, including an issue over "unreliable airspeed".
Passengers on that flight said that the plane pitched violently and many passengers were screaming and sick.
The accident has also resurrected concerns about Indonesia's poor air safety record which until recently saw the country's carriers facing years-long bans from entering European Union and U.S. airspace.
Items fished out of the sea showed wallets and other personal effects, including a child's Hello Kitty purse.
"In principle, all data we have obtained, including flight data and air navigation, and also from other sources - we find that there have indeed been problems" with the plane, Satmiko said.
The flight that used Boeing 737 Max 8 plane crashed in waters off West Java province's regency of Karawang at around 06:30 a.m. on Monday (2330 GMT Sunday).
National Transportation Safety Commission (KNKT) Deputy Director Haryo Satmiko told CNN that it will take two to three weeks to read the data from flight data recorder, and a further two to three months to analyze it.
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Investigators said the damage suffered by the first data device reflected the severity of the impact.
Divers are still searching for the cockpit voice recorder.
The seafloor is just 30 m down, but strong currents and nearby energy pipelines have hampered the search for the aircraft operated by budget carrier Lion Air, which was heading for the tin-mining town of Pangkal Pinang when it crashed.
Exactly what caused the plane to go down is still unclear but officials said the plane had experienced technical problems the day before the crash.
The airline said the issue had been resolved after the flight "according to procedure".
More than 60 body bags containing human remains have been sent to police medical experts for identification since the search began, but as of Thursday only one victim has been identified and buried.
Ningsi Ayorbaba weeps as she await news of her husband Paul Ferdinan Ayorbaba, a victim of Lion Air flight JT610. However, the Boeing plane that crashed in this case was brand new.
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Data from flight-tracking websites shows both flights had highly erratic speed and altitude after takeoff, though confirmation is required from data recorded by the aircraft's "black box" flight recorders.