A large whale rescued in waters off Sabah by officials and tourists was on Sunday found dead in the same area where it was trapped, WWF-Malaysia said.

WWF-Malaysia's marine coordinator, Ken Kassem, who helped to rescue the Bryde's Whale, rarely seen in Malaysian waters, said he had received reports it was found dead on Sunday morning.

"We got reports from numerous people that it was back in about the same place and it was dead," Kassem told AFP .

"Government agencies are working to remove the remains and dispose of them. It's being towed to be anchored offshore, where it can hopefully sink and decompose where it naturally would," he said.

Villagers on Gaya island, near where it had been stranded, said they saw the whale early Sunday lying on its side with the water around it turning red from blood, the Star daily reported on its website.

"We were all hoping it wouldn't happen ... It's common enough," Kassem said of the whale's return. "I think everybody is pretty sad that it did."

Divers and wildlife officials had worked tirelessly to free the 20-metre long whale. It was sighted Thursday stuck on a coral reef in shallow waters between Gaya and Sapi islands off Sabah's coast.

"It was a big team with a lot of government agencies, NGOs and private citizens," said Kassem.

After an initial failed attempt, the whale, which suffered cuts from coral trapped under its body, was finally towed by a tugboat to deeper waters in the South China Sea on Friday evening, to the elation of rescuers.

"I was on the tugboat when we were towing it off the reef the second time and I could hear people in the smaller boats closer to the whale cheering at one point," Kassem said.

"Once we all got back together, everybody was very happy to have got it off the reef," he said.

Kassem said it was unclear why the whale had returned.

"We really wanted it to swim off and live happily ever after. Sometimes that's not the case," he said.

Bryde's Whales have been the target of intensive whaling. The International Union for Conservation of Nature and Natural Resources has put it on a list of threatened species.