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, reports the BBC.
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 to fly to Mali.
The French authorities have not yet commented.