Mali has sent back two people who were deported from France on the same planes they arrived on, questioning whether they were even Malian citizens.
The pair were flown to Bamako using European travel permits or “laissez-passez”, not passports or other Malian papers, the government said.
The government said it could not accept people “simply assumed to be Malian”.
Recent reports of a deal with the EU to repatriate failed Malian asylum seekers have sparked protests.
In a statement, the Malian government condemned the use of the European “laissez-passez” in cases of expulsion, describing it as “against international conventions”.
It also warned airlines not to let people using the document fly to Mali.
There is a large Malian community in France, the former colonial power, which supports their relatives back home by sending money.
More than 360,000 people have reached Europe by crossing the Mediterranean this year, Many pass through Mali on their way although Malians are not among the 10 nationalities most likely to attempt the journey.
Mali has denied that it agreed to enable the return from Europe of Malian migrants as part of a deal that was heralded in December by senior European diplomats as the first of its kind.
A $1.9bn (£1.2bn) European Union-backed fund to tackle African migration was announced in November 2015, with African leaders agreeing to allow the return of failed asylum seekers in return for development aid.