Fifteen-year-old Ram Bahadur Bamjon has not been seen since early Saturday, said Hari Krishna Khatiwada, a district official of Bara, 150 km (95 miles) southeast of Kathmandu.
The boy had been meditating there without food or water since May. Some of his followers are also missing.
"So far we have found no trace of them," Khatiwada said.
Sitting cross-legged beneath a "pipal" tree, which is sacred to Hindus, Bomjon drew more than 100,000 people to the dense forests in southeastern Nepal.
But visitors were only allowed to see him from 50 metres (165 feet) away and the boy was hidden from public view at night behind a curtain drawn by his followers.
(If they don't find him, here is another myth to add to the list?)