At least 31 people died in Kourakou and 13 in Tondobi, according to officials. Photo has been used for illustrative purposes only.

The provisional toll of "this despicable and barbaric attack" which targeted the villages of Kourakou and Tondobi in northeast Burkina Faso overnight on Thursday "is 44 civilians killed and others wounded," said Rodolphe Sorgho, lieutenant-governor of the Sahel region.

Sorgho said that 31 people had died in Kourakou and 13 in Tondobi.

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The regional official said that an army offensive put "out of action the armed terrorist groups" that carried out the killings.

The governor also assured that "actions to stabilise the area are under way".

The impoverished Sahel country is grappling with a seven-year-old campaign by militants linked to Al Qaeda and the Daesh group.

Burkina Faso coup leader Capt. Ibrahim Traore participates in a ceremony in Ouagadougou. File/AP

A resident of Kourakou told the media that "a large number of terrorists burst into the village" late on Thursday.

"All night long, we heard gunfire. It was on Friday morning that we saw that there were several dozen dead," he added.

Locals said the village had been targeted in retaliation for the lynching of two militants a few days earlier who had tried to steal cattle.

It was one of the deadliest attacks since Captain Ibrahim Traore came to power in a coup last September,

In February 51 soldiers were killed in an attack on Deou, in the far north of the country.

The latest twin attacks happened close to the village of Seytenga, where 86 civilians were killed last June in one of the bloodiest attacks of a long-running insurgency.

Supporters of Capt. Ibrahim Traore wave a Russian flag as they go through the streets of Ouagadougou, Burkina Faso.

Burkina Faso's new military chief this week vowed to step up a "dynamic offensive" against militants following a string of insurgent attacks since the start of the year.

"The dynamic offensive under way in the past few weeks will be stepped up to force armed groups to lay down their weapons," said Colonel Celestin Simpore after a handover ceremony following his appointment last week.

Since the militants launched their campaign from neighbouring Mali in 2015, more than 10,000 civilians, troops and police have been killed, according to one NGO estimate, and at least two million people have been displaced.

Official figures say militants effectively control about 40 per cent of the country.

Frustrations within the military led to two military coups last year. Traore, who came to power in September, has vowed to fight back and recover conquered territory.

But the militants have carried out a succession of raids and ambushes since the start of the year, inflicting heavy tolls on civilians and military-escorted convoys.

Burkina's beleaguered army has recently acquired foreign-made drones, and regularly issues video footage of strikes against purported terrorists and troops described as reconquering and securing lost territory.

Since Traore seized power last year, the activities of all political parties and civil society organisations in the country have been suspended.

Agence France-Presse