French investigators will examine black box recordings from a fatal collision between two helicopters in Mali on November 25 that killed 13 soldiers.

Colonel Frederic Barbry told French media that the bodies of the soldiers - killed during an operation against jihadists in the central African nation - would soon be repatriated to France.

The accident marked the largest single loss of French troops since the country intervened in Mali in 2013 to root out militants allied to al-Qaida and the Islamic State (IS).

The helicopters, a Tigre and a Cougar, collided as they provided air support to soldiers on the ground who were tracking militants.

Armies minister Florence Parly said at a press conference that it was with "profound sadness and great emotion" that they learned of the incident.

Read more: France's war in Mali: Why are French troops still fighting jihadists in the Sahel?

Parly said the operation occurred during "total darkness" which "considerably complicated the operation".

Ground troops called in the air support due to the darkness.

Thirteen French soldiers killed in Mali when their helicopters collided at low altitude as they swooped in to support ground forces engaged in combat with Islamist militants. Ministere des Armees/Handout via REUTERS

Both helicopters' black boxes were recovered after the collision, François Lecointre, the chief of defence staff, said at a press conference with Parly. The government has launched an investigation into the incident.

A commemoration ceremony will take place at the Invalides in Paris in the days to come.

France has 4,500 troops stationed in Mali as part of Operation Barkhane, where it is fighting jihadists allied to the Islamic State militant group (IS). Lecointre specified that the operation on Monday was against a group affiliated with IS.

French paratroopers had been tracking the terrorists for several days.

Parly defended France’s mission in Mali saying they were there to “protect Europe from the scourge of terrorism”.

It followed a campaign in 2013, Operation Serval, that targeted Tuareg rebels and Islamist fighters based in Mali's northern desert.

The soldiers killed were named as ADC Julien Carrette, CNE Benjamin Gireud, BCH Romain Salles de Saint Paul, CNE Clement Frisonroche, CNE Nicolas Megard, CNE Romain Chomel de Jarnieu, LTN Pierre Bockel, LTN Alex Morisse, MCH Jeremy Leusie, MDL Alexandre Protin, MDL Antoine Serre, MDL Valentin Duval, SCH Andrei Jouk.