Philippe Verdon
Serge Lazarevic (left) and Philippe Verdon were kidnapped by Aqim in Mali in 2011 (Reuters)

A French hostage found dead in Mali was executed by a shot to the head, a post mortem examination has revealed.

Philippe Verdon, 53, was kidnapped by Islamist militants with Al-Qaeda in the Islamic Maghreb (Aqim) in eastern Mali in November 2011, along with another French citizen.

Aqim said it had executed Verdon in retaliation for France's military intervention in the western African country in March but the body was retrieved near the northern town of Tessalit only a few weeks ago.

French president François Hollande vowed to punish those responsible.

"After the return of the body to France, the autopsy was able to establish that Philippe Verdon was murdered by being shot in the head," the Paris prosecutor's office said.

There had been speculation that Verdon, who was suffering from an ulcer and tachycardia when abducted, had died of natural causes and the Islamist group had used his death as propaganda.

Pascal Lupart, the director of a support group set up to get Verdon freed, said he was "certainly executed because he was weak."

Verdon, a geologist, was reportedly on a business trip when he was abducted from his hotel in the city of Hombori, together with Serge Lazarevic. Family and friends denied that the two had links with mercenary groups or the secret services.

Lazarevic remains in captivity as one of seven French nationals held by Islamist groups in Mali.

"The government is doing all it can to assure their freedom and return to France," Hollande said.

Paris sent troops to Mali to fight an Islamist insurgency which threatened to overrun the capital of Bamako in January.