Fishermen from the village of Kg Tituru Laut towed the whale shark to shore with the help of boats.
A tractor helped to take it to a burial site about a kilometre away.
Manana Borneo Resort operator Sofian Abdul Aziz said the whale shark was discovered around 8.30am on Sunday and could have died soon after.
"We tried to get help from the Fisheries Department, but they did not come," he said, adding that he had to call State Tourism, Culture and Environment Minister Datuk Masidi Manjun for help.
The Wildlife Rescue Unit under the Ministry arrived on Tuesday, but the carcass had already been buried by villagers by then as it was beginning to decay.
According to Sofian, whale sharks are a common sight in the area between Feb and May. He said the whale shark might have been dying and was heading towards the shore.
"Fishermen told us that it was still alive in the nets but it appeared lifeless after a while," he added.