Pramote Chanthamit, president of Nonglalok Sub-District Organisation in Rayong province, said a flash flood inundated a crocodile farm belonging to Paiboon Yongchaihirun.
Mr Pramote said floodwater broke the pond and the farm owner told him that four baby crocodiles were missing.
The official said the sub-district administration dispatched a disaster-response unit to search for the animals and two were found after being reported by local villagers.
He said the first was 1.5 metres long, and another was 70 centimetres in length.
Mr Pramote said he believes two missing crocodiles are adult, and instructed the authorities to remain alert and continue searching for the missing reptiles.