Thirteen French soldiers were killed in Mali when two helicopters collided during an operation against jihadists in the country's restive north, officials said Tuesday, the heaviest single loss for the French military in nearly four decades.

The accident occurred late Monday when three helicopters and a squadron of Mirage jets arrived to support ground troops pursuing Islamist extremists in the Liptako region, near the borders of Burkina Faso and Niger, the defence ministry said.

The accident brought to 41 the number of French troops killed in the Sahel region since Paris intervened against al-Qaeda-affiliated jihadists in Mali in 2013.

It also underscored the challenge for France of trying to control an insurgency in an area the size of Western Europe as a time of escalating violence.

Defence Ministry Florence Parly said Monday's operation was particularly risky because it took place in "total darkness" on a moonless night, but the exact cause of the collision remains unknown.

Shortly after troops engaged the insurgents, who fled on motorbikes and in a pick-up truck, a Tiger attack helicopter collided with a Cougar military transport helicopter, killing all onboard the two aircraft.

Mali has been besieged by militants carrying out deadly strikes against army bases and other targets in recent weeks, a flare-up of violence despite years of efforts to stem the attacks.

Parly told reporters President Emmanuel Macron would lead a commemorative service for the soldiers at the Invalides military hospital and museum in Paris "in the coming days".

General Francois Lecointre, speaking alongside Parly, said the "black box" flight data recorders had been recovered from both aircraft. He did not identify the insurgents, but said the Islamic State in the Greater Sahara (ISGS) - an affiliate of the group active in Iraq and Syria - was the main rebel force in the area.