The attackers went on the rampage in several villages in the districts of Miudumbe and Macomia, killing civilians, abducting women and children and burning down homes, according to Bernardino Rafael, commander-general of Mozambique's police force.
"They burned the houses then went after the population who had fled to the woods and started with their macabre actions," he told local media.
Journalists in northern Mozambique said some people were herded onto the local football field in the village of Muatide and killed there.
On Friday night, gunmen fired shots and set homes alight when they raided Nanjaba village, according to the state-owned Mozambique News Agency, which quoted survivors saying two people were decapitated there and several women were abducted.
On Monday, aid workers and security officials say they found dismembered bodies of at least five adults and 15 boys among trees in the Muidumbe district.
"Funerals were held in an environment of great pain," an aid worker told the news agency. "The bodies were already decomposing and couldn't be shown to those present."
One resident in the main provincial port, Pemba, about 289km south of where the beheadings took place, told the Daily Telegraph that: "Many people arrived here in the last two days as something bad happened up north."
The resident added that people were fleeing the north "all the time" and heading to Pemba.
"Some are coming here by boat and this can take several days and they often arrive desperately hungry and dehydrated."