A government spokesman during the weekend said President Mohamed Ould Abdel Aziz was shot at a military checkpoint by guards who didn't "recognize his convoy," The Guardian newspaper in London reports.
He was apparently wounded in the arm or abdomen, though a spokesman said his injuries weren't life threatening.
He was quoted as saying in a national address that he was "doing well."
"I want to reassure everyone about my state of health after this incident committed by error by an army unit," he was quoted as saying.
The Guardian reports he was flown to France for additional medical treatment. The report cited residents who noted the president is seen frequently in public with only a small security detail.
Mauritania declared parts of its desert a demilitarized zone in 2008 to combat terrorist groups like al-Qaida in the Islamic Maghreb, the North African branch of al-Qaida.
The president took office following a 2008 coup. Few of Mauritania's governments were elected or completed their full terms, falling to a series of coups since independence in the 1960s.