The foreign ministry said the bodies of Claude Verlon and Ghislaine Dupont had been found.
Earlier, radio station RFI confirmed the kidnappings on its website, saying that the two were taken at 1 pm by armed men in Kidal and had not been heard from since.
The ministry said in a statement that French intelligence services along with Malian authorities "are putting everything in place so that light can be shed as quickly as possible on the circumstances of their deaths."
A Malian military head, Col Mamari Camara, said he had received a phone call in the afternoon from his men in the field confirming the two reporters had been taken.
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The two were grabbed by several armed men in a 4x4 after they finished an interview with a Tuareg rebel leader, a Kidal city official said on condition of anonymity because he was not permitted to speak to the press.
Northern Mali last year was seized by a faction of al-Qaida which has used kidnappings of foreigners, especially French citizens, to bankroll its operations.