Nigeria-based Boko Haram fighters have carried out their first attack inside Chad, killing as many as 10 people in an early morning strike on a village and military camp on the shores of Lake Chad, a security source has said.

Friday's pre-dawn attack left civilians and soldiers dead and most of the village of Ngouboua torched before the fighters were pushed back, the source told the AFP news agency on condition of anonymity.

At least 30 attackers struck after crossing the lake from Nigeria's Baga in large canoes and set ablaze nearly two-thirds of Ngouboua - about 20km east of the Nigerian border - where around 7,000 Nigerians have taken refuge.

Chadian military aircraft carried out airstrikes against the fighters, destroying their vessels, the security source added.

"We sent in our air force and they neutralised the three pirogues. We are still combing the area," a spokesman for the armed forces said.

Residents are now fleeing the village and a Chadian humanitarian vehicle was attacked as it tried to escape, UN refugee agency spokesman Adrian Edwards told reporters in Geneva.

The armed group has carried out several cross-border attacks in neighbouring countries, who have launched a regional operation to combat the group.

Last week, Chad army claimed to have killed scores of Boko Haram fighters.

Boko Haram, which has been designated by the US as a "terrorist" organisation, has been fighting since 2009 to establish sharia law in all 36 states of Nigeria, which is roughly equally divided between a mainly Christian south and a largely Muslim north.

The Nigerian government has since May 2013 declared a state of emergency in Adamawa, Borno and Yobe, the three states where most of the deadly attacks have happened.