Broadcaster France 24 reported the confirmation after French President Francois Hollande said earlier there was a strong possibility the body was that of the 53-year-old French geologist who was one of two French citizens kidnapped by al-Qaida in the Islamic Maghreb in Hombori in November 2011.
Verdon's captors said in March they killed him because they believed him to be a French spy. They said the execution was also in response to France's military intervention in Mali beginning in January.
"We found a body 10 days ago in northern Mali. We are doing everything possible to confirm that this could be, alas, the body of Philippe Verdon," Hollande said at the Mali Embassy in Paris before the body was positively identified.
"We will then determine the cause of death and nothing will go unpunished."
AQIM has eight European hostages, including five French nationals, Radio France Internationale reported.