Making such allegations while French troops are risking their lives to protect citizens was "indecent," Defence Minister Florence Parly's office said in a statement sent to AFP.
"Rather than channelling and spreading false accusations, we expect the ambassador of Mali to devote all his energy to implementing the Pau summit and achieving success for everyone," the statement said tartly, referring to a meeting between France and its Sahel allies last month.
France has 5,100 soldiers in Operation Barkhane, a mission to roll back jihadism in Mali as well as Burkina Faso, Niger, Mauritania and Chad.
But its presence has been criticised by some in the region, who balk at the prominent military role played by a former colonial power.
Last month, hundreds of people gathered to protest the presence of French soldiers, holding aloft placards reading "Down with France, Barkhane must leave" and "France is a brake on our development."
Such criticism has riled French officials, especially after 13 soldiers were killed in a helicopter collision in Mali while pursuing jihadist fighters -- the deadliest toll for the French military in nearly four decades.
On Wednesday, Mali's ambassador to France Toumani Djime Diallo complained to the French Senate of "problems" caused by what he described as French Foreign Legion soldiers deployed on Malian soil.
He pointed to "excesses" in the Malian capital.
"At times you see them in the red-light districts of Bamako, their bodies completely covered in tattoos, behaving in a way that does not correspond to the [French] army we know," Diallo said. "It makes people afraid, it makes tongues wag."
Parly's office said such accusations were false as there were "hardly any" French soldiers stationed in Bamako.
The charges were also "unacceptable and indecent when France has resolutely committed itself to fighting terrorist groups that threaten the people of the Sahel."
France's deployment is by far the largest foreign contribution to the fight against extremists aligned with Al-Qaeda and the Islamic State group.
Last month, French President Emmanuel Macron and the leaders of five Sahel countries pledged to jointly bolster efforts against jihadists fighting the increasingly deadly insurgency.
Macron has denounced "foreign powers" for stirring up anti-French sentiment amid reports that Russian paramilitary fighters were increasingly active in the Sahel.
And he has complained of a lack of "clear political condemnation of anti-French feelings" on the ground, saying he was loath to send soldiers to countries where their presence was not "clearly wanted."
Despite the French presence and a 13,000-member UN peacekeeping force in Mali dubbed MINUSMA, the conflict that erupted in the north of that country in 2012 has since spread to its neighbours, especially Burkina Faso and Niger.
Thousands of civilians and hundreds of soldiers have been killed and more than a million people have been displaced. France has lost 41 soldiers.