The deadly sinkings, whose victims include six children, come as millions travel across the country for the Eid holiday season.
The week of Eid, which marks the end of the Muslim holy month of Ramadan, is the busiest travel period of the year in the world's most-populous Muslim country, when most people abandon big cities and return to their hometowns to celebrate with family.
A boat carrying 48 people sank on a river on the island of Sumatra late Wednesday after experiencing engine trouble, leaving six children and one adult dead, a local police said.
He added that police were scouring the river to find 13 still missing.
A ferry carrying 70 people on a river in the Indonesian part of Borneo island sank on Tuesday, with the final death toll put at 18. The rest survived.
"By this morning, all 18 bodies had been recovered," the local head of search and rescue, Wasino, who goes by one name, told AFP.
The National Disaster Management Agency said police were questioning the ferry crew as there were reports that the ferry might have been operating at overcapacity.
Boat accidents in the vast Indonesian archipelago are not uncommon.
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