At least 43 people were killed and six others injured after unknown gunmen attacked at least two villages in Burkina Faso's northern region near the border with Mali, according to a statement by the government.

The villages are mainly inhabited by the Fulani community which has been accused of having links with jihadists prompting other communities, such as the Dogon and Bambara, to form self-defense groups.

"On Sunday, attacks were carried out on the villages of Dinguila and Barga … in Yatenga province. The provisional toll is 43 victims," the statement read in part.

The injured were taken to a hospital in the neighboring area of Ouahigouya after the military was deployed to secure the villages.

No group was accused of perpetrating the attacks in the statement and no group claimed responsibility for them.

Burkinabe President Roch Marc Christian Kaboré condemned the attacks, which are one of the worst in the country in the past year.

"I condemn in the strongest terms the heinous attack perpetrated on Sunday by unidentified gunmen, which killed 43 people in the northern town of Barga. I offer my sincere condolences to the grieving families," President Kaboré tweeted.

Kabore also declared a 48-hour national mourning period and dispatched the Ministers of Defence and Territorial Administration to Barga to take stock of the situation.

Reprisal attacks against the Fulani have spiked in the wake of a revolt in 2012 which broke out leaving thousands of people dead and thousands of others displaced. These attacks have largely pitted Dogon hunters against Fulani herders.

Last month, gunmen killed 31 people in the Ogossagou village in central Mali, mainly inhabited by the Fulani community, and burnt crops and huts. About 28 others were reported missing following the attack.

Ogossagou village, near the border with Burkina Faso, is the same one in which 160 Fulani were killed in March last year by suspected Dogon militia.