In response to a Boko Haram attack on a Chadian military base that killed at least 40 last week, Chad's army on Wednesday launched an airstrike pummelling Tilma island in the Kukawa district on the Nigerian side of Lake Chad.

That hit and killed fishermen tending to their catch, fishermen and anti-jihadist militia said -- accusations Chad rejects.

"Chad firmly denies recent reports of attacks allegedly carried out by the Chadian army against civilians, in particular fishermen in the Lake Chad region," government spokesman Abderaman Koulamallah said on Friday in a statement.

"The operations carried out so far have targeted well-identified jihadist groups," he said.

The government spokesman insisted Chad's army operations were "organised and disciplined, and scrupulously careful never to target civilians".

But speaking on condition of anonymity, a Chadian general staff officer who confirmed the strikes to AFP raised the possibility the army made a mistake.

"Boko Haram fighters often blend in with the fishermen and farmers whenever they commit their crimes. It is therefore difficult to distinguish between the population and the terrorists," the officer said.

Babakura Kolo, an anti-jihadist militia leader in Nigeria, echoed those concerns.

Chad's fighter jet "mistook the fishermen for Boko Haram terrorists who attacked a military base inside Chad on Sunday," Kolo said.

Fisherman Sallau Arzika, who escaped the airstrike and made it back to the garrison town of Monguno, told AFP "the fighter jet encircled Tilma before beginning to drop bombs while people ran in all directions for cover".

"A large number of fishermen were killed. No one can give an exact number because bodies are still scattered across Tilma."

Chad's government denounced the accusations as "false allegations" designed to "sow confusion and destabilise public opinion".

Besides killing around 40 people, Boko Haram's Sunday raid on a base in the Lake Chad region also left dozens wounded, with the group claiming responsibility for the attack in a propaganda video released on Monday.

Chadian President Mahamat Idriss Deby, who visited the military base after the jihadist attack, is said to be "personally" leading the army's counter-offensive against the militant group.

Located at the intersection of Niger, Nigeria, Cameroon and Chad, Lake Chad is dotted with islands sheltering fighters from Boko Haram and its splinter group, the Islamic State in West Africa.

Since emerging in Nigeria in 2009, Boko Haram has spread to neighbouring countries while killing some 40,000 people and displacing more than two million.