The MA-60 aircraft, operated by state-owned Merpati Nusantara airlines, was coming in to land at an airport in East Nusa Tenggara province when the accident happened, said transport ministry spokesman Bambang Ervan.
Pictures showed the Chinese-made turbo-prop plane lying on its belly on the runway with its engines jammed facedown into the tarmac and its wings bent forward.
An increasing number of planes are taking to Indonesia's skies to feed growing demand from a booming middle class, but the vast archipelago has one of Asia's worst aviation safety records.
Today's accident happened as the plane, which was on a domestic flight from the central island of Flores, came into land at El Tari airport in Kupang city at 9:40 am (0710 IST), Ervan said.
There were 52 people on board, 46 passengers and six crew, said Merpati spokesman Herry Saptanto.
"Two passengers sustained minor injuries from pieces of glass but they have left hospital and are now fine," he told AFP.
In May 2011 an MA-60 operated by Merpati crashed in West Papua province, killing 25 people.
Following that accident, authorities banned the plane -- manufactured by Xi'an Aircraft Industrial Corporation -- from landing at three airports with difficult approaches.
However, Saptanto said today the ban had been lifted six months earlier. El Tari was not one of the airports affected by the ban.
Merpati has been banned from flying in European Union airspace since 2007.
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