They were Mohamad Azfar Tahir, 23, from Kuala Lumpur and Mohammad Ezzaq Azumi, 23, from Kelantan, said Malaysia’s ambassador to Indonesia, Zahrain Mohamed Hashim.
They are believed to have come to Flores with three other friends for a holiday.
Both men were said to be missing after jumping into the waterfall area after arriving at the spot at about 10.30am on Saturday.
A local man, Wenseslaus Hendro Akung, 39, believed to be a tour guide, has also gone missing when he jumped into the water to try to save the two men.
The other three Malaysians sought the assistance of the public and contacted the police.
Zahrain said a search and rescue operation by the local authorities took place from 3pm to 5pm, when darkness fell. The search will resume today.
-BERNAMA
