Mauritanian troops backed by French intelligence and special forces killed six fighters from Al-Qaeda's North Africa wing, AQIM, in an attack on a base in Mali on Thursday, an escalation in African and European responses to the region's Islamists.
"We have no proof of life or death of Michel Germaneau," a French defense ministry source said. "There was hope that (he) was in this camp, (but) when we arrived he wasn't there."
A Mauritanian security source said earlier on Saturday the operation against Al-Qaeda had finished after four days.
Another security source said that the raids had continued some 200 km (124 miles) into Mali after Thursday's pre-dawn attack on a group of Islamists who are believed to be holding the 78-year-old French hostage in the desert Sahel region.
The French defense ministry source said the operation was launched after AQIM failed to provide proof that Germaneau was alive or engage in negotiations over him.
A retired engineer, Germaneau was kidnapped by the group in April. AQIM had set France a deadline of next week to agree to a prisoner swap, saying it would otherwise kill him.
The operation follows calls for better international cooperation against AQIM, which was previously focused on Algeria but now has two factions that are increasingly active in remote desert regions of Mauritania, Mali and Niger.
Paris has said it gave technical and logistical support to Mauritanian forces in an operation aimed at preventing an attack by AQIM on Mauritania. The French Defense Ministry source said between 20-30 French operatives had taken part.
The raid could also have been a failed bid to rescue Germaneau, who was kidnapped in Niger and is believed to be in the hands Abdelhamid Abou Zeid, leader of the more hard-line of the two AQIM factions operating in the Sahara.
Late on Friday, Mauritanian state television broadcast images of dead AQIM fighters, two of the group's captured four-wheel drive vehicles and their destroyed desert camp.
Mauritania said it had gathered significant amounts of explosives, ammunition and intelligence from the raid, but four fighters, one of whom was wounded, escaped.
The operation appeared to anger official Mali, which was not involved, and Spain, which also has hostages held by another Al-Qaeda faction in the region. The French source said both countries had been informed of the operation.
Mauritania's defense minister traveled to Mali on Friday, but no news has emerged from the visit. Spain has said that its citizens, two aid workers captured in Mauritania last year, are being held by a different group than the one attacked this week.
Le Monde newspaper said on Saturday AQIM's demands from France — which include the freeing of Rachid Ramda, jailed for his involvement in three Paris bombings — meant that any exchange was unlikely in any case.
Islamists in the Sahara have so far not staged any large-scale attacks, and analysts say they have concentrated largely on collecting revenues from ransom payments and the smuggling of goods, including cocaine.
But, fearing these groups could become too powerful in vast desert zones governments have little sway over, Western nations led by France and the United States have stepped up involvement in the region and are seeking to forge better coordination.