The Italian national, identified as Giuseppe Favaro, has been in custody in the small central African nation since late October after he was caught trying
to export two skulls to Thailand.
"Everyone in Burundi is stunned and shocked by this, because it's the first time we've had such a thing. Even anthropologists stopped doing this kind of
thing a long time ago," police spokesman Helmenegilde Harimenshi said.
He said Favaro, who has lived in Burundi for around 10 years, had been buying the skulls for around €40 each and selling them for €300.
However it remained a mystery as to what the skulls would be used for and why they were being sent to Thailand, adding that Burundi had asked Interpol to help with the investigation.
"We discovered a package at Bujumbura airport containing two skulls, and investigations established it was sent under a false name by Giuseppe Favaro, an Italian," Harimenshi said.
"Police then discovered 36 human skulls during a search of his house, along with other incriminating evidence," he added.
Police said three accomplices had also been arrested.