European governments accuse the Minsk government of luring refugees from the Middle East to Belarus to send them across the border to the European Union soil in retaliation for sanctions.
Turkish and Polish foreign ministers discussed the refugee crisis at the Poland-Belarus border.
On Wednesday's phone call, sources say, Turkish top diplomat Mevlut Cavusoglu told his counterpart Zbigniew Rau that Ankara is not part of the problem as it is displayed.
Cavusoglu underlined that Ankara rejected the "baseless allegations against Turkey and Turkish Airlines."
The Turkish foreign minister also said that he invited a Polish technical team to Turkey and stressed the public should be informed properly.
Poland and the EU have accused Belarusian President Alexander Lukashenko of trying to retaliate against EU sanctions by deliberately inviting and forcing refugees toward the Polish border.
Turkish Airlines refutes claims
Turkey's national flag carrier refuted allegations that the company was aiding in illegal immigration to Belarus amid the refugee crisis at the border.
"The news in media outlets do not reflect the truth," said Turkish Airlines on Tuesday adding the company's operations are in "cooperation with international authorities that take all security sensitivities into account."
EU countries bordering Belarus – Lithuania, Latvia and Poland – have reported a dramatic spike in the number of irregular crossings since August.
NATO and the EU consider Belarus’ approach toward refugees an effort to destabilise and undermine security in the bloc through non-military means.
According to the latest EU figures, 7,935 people tried to enter the bloc via the Belarus-EU border so far this year, up sharply from just 150 last year.
On Monday, Polish authorities stepped up border protection and mobilised more than 12,000 troops after a large group of refugees started marching toward the country’s frontier with Belarus accompanied by the Belarusian military.