Boko Haram militants attacked two villages in southern Niger's Diffa region overnight, killing at least 30 civilians, two security sources said on Thursday.

It was the second major cross-border attack by the Nigerian Islamist group this week, following twin suicide bombings in Chad's capital on Monday that killed at least 34 people.

The attackers drove into the villages in the Gueskerou area with cars and motorbikes and shot residents before setting fire to the mostly straw thatched houses where others were hiding, the sources said.

"In all, at least 30 were killed. Some of them died when the houses were set alight," said one of the security officials. The source said he expected the death toll to rise because a number of survivors had serious burns.

Gueskerou is along the banks of the Komadugu River separating Niger from Nigeria.

Despite a regional military operation to beat back Boko Haram, southern Niger has been attacked dozens of times this year. Its government has declared a state of emergency for the region and has arrested more than 600 people it accuses of links to the group.