He added that the location of the crash site is about two nautical miles from where it lost contact with air traffic control and that the aircraft is likely to have sunk to a depth of about 30 to 35 metres underwater.
Local media reported the pilots requested a return to Jakarta before losing contact with air-traffic controllers.
The jet, which had been recently grounded for repairs, vanished from radar just 13 minutes after taking off from the Indonesian capital, plunging into the ocean.
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Photos posted on the Twitter account of the national search and rescue agency Basarnas showed six body bags being brought to shore at Tanjung Priuk port. Indonesia energy firm Pertamina official says debris, including plane seats, found near its offshore facility in Java sea.
What do we know about this aircraft?
"We hope, we pray, but we can not confirm", He said, adding that no distress signal had been heard from the plane's emergency transmitter.
"The South African government wishes the Indonesian government and people, particularly the affected families, strength during this time of grief", said Ndivhuwo Mabaya, spokesman for the national department of global relations and cooperation (Dirco).
Indonesian rescuers have found passengers' belongings and debris, but are yet to locate the main body of the plane.
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According to officials, no distress signal was received from the aircraft's emergency locator transmitter.
Air travel is crucial in Indonesia, a vast archipelago of more than 17,000 islands that stretches about 5,100 km (3,170 miles) from east to west, nearly the distance between NY and London.
The Indian Embassy in Jakarta tweeted, "Our deepest condolences on the tragic loss of lives in the Lion Air Plane crash, off the coast of Jakarta today". The incident is also a blow to the country's aviation safety record after the lifting of bans on its airlines by the European Union and US.
The National Search and Rescue Agency's deputy chief, Nugroho Budi Wiryanto, said some 300 people including soldiers, police and local fishermen are involved in the search. The plane serving Lion Air flight JT 610 was configured to seat 189 passengers, said aviation consultant Gerry Soejatman.
A passenger plane carrying 188 people has crashed into the sea off Jakarta.
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