In one instance, a three-month-old calf was found alongside the body of its mother, apparently trying to wake her.
Sabah Environmental Minister Masidi Manjun said it was "a sad day for conservation and Sabah".
Sen Nathan, head veterinarian at the Gunung Rara Forest Reserve in Malaysia's Sabah state on the island of Borneo, said the elephants were all thought to be part of the same family group, and were aged between four and 20.
The bodies of four were found last week but then officials found another four animals dead or dying two days later.
Laurentius Ambu, Sabah's wildlife department director, said two "highly decomposed elephant carcasses" had been found earlier in the year.
"We believe that all the deaths of these elephants are related," he said.
The animals still had their tusks, indicating that they had not been killed by poachers, and none had gunshot wounds.
There are thought to be fewer than 1,500 Borneo pygmy elephants in the wild
Samples have been sent for testing, but Mr Nathan said the damage evident in the elephants' digestive systems had led officials to "highly suspect" acute poisoning. Tests will confirm whether they could have been deliberately poisoned.
"It was actually a very sad sight to see all those dead elephants, especially one of the dead females who had a very young calf of about three months old. The calf was trying to wake the dead mother up," he said.
The WWF estimates that there are fewer than 1,500 Borneo pygmy elephants in the wild, most of them in Sabah state.
They are the smallest elephant subspecies, with babyish faces, long tails and straight tusks. They are threatened by logging, hunting and increasing contact with humans.
Mr Masidi said the death of "these majestic and severely endangered Bornean elephants is a great loss to the state".
"If indeed these poor elephants were maliciously poisoned, I would personally make sure that the culprits would be brought to justice and pay for their crime," he said.