The magnitude 7.5-quake and a subsequent tsunami razed swathes of the city of Palu on Sulawesi island on September 28.
A total 2,065 bodies had been recovered since the twin disaster, the disaster agency said Thursday.
But authorities fear 5,000 more could be buried beneath the ruined city, where entire villages were swallowed.
Rescuers had struggled to find remains in the twisted wreckage, a job made worse as mud hardened and bodies decomposed in the tropical heat.
"The search and rescue (SAR) operation for the victims will end this Thursday afternoon," SAR field director in Palu, Bambang Suryo, told AFP.
"Considering the difficulty on the ground, we really need to consider the health and safety of our rescue personnel."
Teams would however remain on standby in Palu until October 26, when a state of emergency is expected to be lifted.
The government earlier indicated that hard-hit areas would be left untouched as mass graves.
Parks and monuments are planned at three of these worst-hit areas -- Balaroa, Petobo and Jono Oge -- to commemorate the possibly thousands of dead who will never be found.
Those zones were all but destroyed by liquefaction, a phenomenon where the brute force of a quake turns soil to quicksand.
More than 200,000 people remain in dire need of humanitarian assistance in Palu, with clean drinking water and medical supplies still in short supply.
The United Nations has sought $50.5 million for immediate relief to help the victims.
Planeloads of donations have flown into Palu from the United States, Australia, the European Union and the Philippines, among many others.
Nearly 80,000 people were displaced by the disaster, many sheltering in tents outside their destroyed homes.
United Nations Secretary General Antonio Guterres will tour the disaster zone with Indonesian Vice President Jusuf Kalla on Friday.
'It will rise again'
Central Sulawesi governor Longki Djanggola said the survivors would be supported in their time of need.
"I am sure Central Sulawesi will rise again," he said in a statement.
Humanitarian efforts have accelerated into the disaster-ravaged city, but the recovery effort was criticised for moving too slowly.
Looters ransacked shops in the immediate aftermath of the disaster, as food and water ran dry and convoys bringing life-saving relief were slow to arrive.
Getting vital supplies to the affected areas proved hugely challenging as flights into Palu were limited by its small airport, leaving aid workers facing gruelling overland journeys.
Indonesia initially refused international help, saying the military had the situation in hand.
Four days after the disaster, once the picture became clearer, President Joko Widodo reluctantly agreed to allow in overseas aid.
But earlier this week foreign aid workers were told to withdraw their personnel, frustrating some groups keen to help out on the ground.
Some foreign rescue teams were unable to access the disaster zone and deploy quickly to help search for the dead and missing.
"We just came here because the government of Indonesia asked for assistance," said Marcus Butler from South African charity Gift of the Givers, which was denied permission to help with the search.
"They say there is no need for aid in Indonesia. But look at all these people," he told AFP.
Indonesia sits along the world's most tectonically active region, and its 260 million people are vulnerable to earthquakes, tsunamis and volcanic eruptions.
Another earthquake rattled the region Thursday, killing at least three people in Java and sending tourists and IMF delegates in Bali for a major summit scrambling from hotels.
The 6.0-magnitude earthquake struck off the coast of Bali and Java islands in the early hours, jolting residents awake and sending them rushing into the streets.
A string of earthquakes in Lombok, in eastern Indonesia, killed more than 550 people over the summer.
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