The chief executive of flydubai, which operates a daily flight to Minsk, said on Monday it only allows passengers with valid travel documents to board its planes.
The EU has threatened to place sanctions on airlines found to be transporting migrants seeking to enter the bloc illegally from Belarus.
EU foreign ministers met in Brussels on Monday to agree on additional sanctions against Belarus over the crisis, during which up to 4,000 people have been stranded in freezing forests on the Belarusian border with Poland.
“Nobody likes to see these things but as for transport of people to Minsk, every passenger we transport has the right documentation, the right visa,” Ghaith Al Ghaith told Reuters at the Dubai Airshow.
“We have never carried a passenger who was illegal under the rules in operation on the day of travel,” he said.
He also called on governments to work more closely with airlines to identify such passengers as “you cannot [always] determine what is people's intent".
“Without tools in our hand, you know, we cannot identify who is who and if there were people who unfortunately suffered from … what we do, we are so sorry for that,” Mr Al Ghaith said.
The airline increased direct services to Minsk in mid-September from several flights a week to a daily service, the website flightradar24 shows.