Bhagirath Singh of West Bengal's Khoribari was paid Rs 1,000 by an unidentified person to smuggle the cranial bones across the border, they said.
The human skulls might have been smuggled for performing tantric rituals, Superintendent of Police Sailesh Thapa said.
Singh was caught by police during a security check near Kakarbhitta customs office in Jhapa district on Monday, about 450 kms east of Kathmandu.
He will be booked under the Public Offence Act as Nepal's law does not specify possession of human body parts as an offence.
Nepalese and Indian citizens often smuggle human skulls to Nepal from Assam, Meghalaya and Mizoram through Kakarbhitta border.