MAPUTO – Thousands of people have flooded Mozambique's northern city of Pemba after brazen jihadist attacks on two towns in the restive region, local and church sources said on Tuesday.

Insurgents descended on Mocimboa da Praia and the nearby town of Quissanga last week, ransacking government buildings and hoisting their flag before retreating.

A shadowy jihadist group has wrecked havoc in northern Mozambique for more than two years, killing more than 900 people, according to the Armed Conflict Location & Event Data Project (ACLED).

The attacks have displaced more than 200,000 people since the start of the insurgency in October 2017, according to local Catholic archbishop, Dom Luiz Fernando.

The displaced have sought refuge in Pemba, the capital of Cabo Delgado province, moving in with families and friends.

Many arrived in boats after the main bridge on the main road connecting Pemba to the north was damaged by floods.

"We have more than 100 families who have welcomed people into their homes," in recent days, said Fakir Rugunate, a senior official in the city's Cairiaco neighbourhood.

Momade Abu reached Pemba on Monday from Quissanga.

"We hope that one day the conflict will end and we can return to our fields," he said.

"Here we are suffering, we have nowhere to sleep, and nothing to eat but the situation is worse where came from," he said.

"We stayed in the bush for two days until (the attackers) left. We left everything behind," he added.

Keeping track of the arrivals has not been easy.

The government has instructed officials in the poor Pemba neighborhood of Paquitequete, where boats dock, to record details of all the arrivals and where they will seek shelter.

"To date we have registered more than 4,000 people - mostly women and children," said a local leader who asked not to be named.

A Catholic source said the church was mobilising aid to support the displaced, but lack of data on their exact addresses made it more difficult to help.

"This is a humanitarian disaster," said a source from the archdiocese of Pemba. - AFP