Bamako blames Paris for committing "frequent violations" of its airspace and collecting intelligence "for the benefit of terrorist groups."
Mali's ruling junta has said France's military pullout after nine years of battling militants in its former colony would usher in an era of improved security in the West African country.
The government "takes note of this final withdrawal", its spokesperson Abdoulaye Maiga said in a statement on Friday.
It "reassures the Malian population that, thanks to the rise in power of the brave Malian forces, more successes will be recorded against the terrorist groups," he said.
"People's security will be considerably improved."
France on Monday said its last remaining troops had quit Mali.
It said its anti-militant Barkhane operation in the Sahel region would retain around 3,000 troops even after the Mali drawdown, many of them based in Niger.
Relations between Bamako and Paris have soured following two military coups in Mali since 2020.
The arrival of Russian paramilitaries in the Sahel country at the invitation of the government was a key factor in France's decision to pull out its forces.
Defence Minister Sadio Camara this week travelled to Russia and was still there on Friday.
On Monday, Foreign Minister Abdoulaye Diop in a letter to the Chinese presidency of the UN Security Council accused France of "acts of aggression" and of backing militants.
Diop claimed that French forces committed "frequent violations" of Malian airspace, suggesting the flights were "to collect intelligence for the benefit of terrorist groups... and to drop arms and ammunition to them".
France responded by condemning the "increasing manipulation of information" about its military withdrawal.