The bus carrying dozens of passengers careered into a 150-metre (500-foot) ravine in South Sumatra province just before midnight (1600 GMT) on Monday and ended up in a river, police said earlier.
Originally the death toll given by police was 24, but the head of the local search and rescue team Berty Kowas said another body was found, taking the number to 25.
"Currently the evacuation is ongoing and some divers are searching (for victims) around the bus," Kowas told Metro TV on Tuesday.
Footage shared by the rescue team showed bodies being taken out of the water on to stretchers.
Police and rescuers were scouring the river and the nearby slopes to look for victims and several passengers were feared missing.
"It crashed into the concrete road barrier before plunging into the ravine. Some people are still trapped inside the bus," local police spokesman Dolly Gumara told AFP on Tuesday, adding no other vehicle was involved.
Search and rescue teams have been deployed to look for victims, Gumara said, adding injured survivors were taken to hospital.
The accident happened in a remote and steep area near the town of Pagar Alam, hampering the efforts to rescue the victims.
According to a passenger manifest, the regional bus left Bengkulu province for Pagar Alam with 27 on board but some survivors told police there were around 50 people inside when the accident happened.
"Some passengers were probably added along the way so there's a possibility some more people are still missing in the river," Gumara said, adding the cause was being investigated.
Traffic accidents are common in the Southeast Asian archipelago, where vehicles are often old and poorly maintained and road rules regularly flouted.
In September, at least 21 people died when a bus plunged into a ravine in West Java's Sukabumi region.
Several months earlier, 12 people were killed and dozens more injured when a passenger tried to wrest control of a bus steering wheel following an argument with the driver on the same toll road in West Java as Thursday's accident. The bus smashed into two cars, causing a truck to roll.
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