Forestry officers in eastern Terengganu state said they had found a specimen which appeared to have the petals of one species but the internal form of another.
It could be a new species, form or variation," South Terengganu forestry official Roslee Jamaludin told the New Straits Times.
"We are excited. We have checked all known Rafflesia species and so far we have not found anything similar. We need to look closer at its characteristics before confirming that it is a new species."
The location of the flower was being kept secret, but Roslee said it was found in the state's Pasir Raja jungle reserve and that it was growing as a climber on a large tree.
Rafflesia flowers are rare but found in several Southeast Asian countries. They weigh as much as 10 kilos (22 pounds) and measure up to one metre (3.3 feet) across, and survive only a few days before dying.
The smell of the opened flower, which is designed to attract insects that pollinate the blossom, is described variously as like fresh cow dung or rotting flesh, and its local name means "corpse flower" or "meat flower."
The species was discovered in 1818 and named after Sir Thomas Stamford Raffles, the founder of Singapore.