Items found included 115 drinking cups, four plastic bottles, 25 plastic bags and two flip-flops.
The carcass of the 9.5m (31ft) mammal was found in waters near Kapota Island in the Wakatobi National Park late on Monday.
The discovery has caused consternation among environmentalists.
"Although we have not been able to deduce the cause of death, the facts that we see are truly awful," Dwi Suprapti, a marine species conservation co-ordinator at WWF Indonesia, was quoted as saying by the Associated Press.
