Frontex is under growing scrutiny over allegations it violated the human rights of certain people seeking asylum while forcefully returning other migrants to non-EU countries.
The EU ombudsman has also said the agency failed to meet transparency requirements.
During a visit with an EU delegation near the Belarusian border in Lithuania, Frontex executive director Fabrice Leggeri said that legal clarification was needed to "know what is possible and what is not" in the EU.
Greek Minister for Migration and Asylum Notis Mitarachi, who also spoke to reporters, said:
"It is clear that the nature of the migration crisis has changed in the last few years. We had a similar experience at the Greek-Turkish borders in March 2020 where migration is now being used by third countries, weaponizing human suffering for geopolitical gains."
Lithuania in August began pushing back almost all Middle Eastern migrants who sought to cross from Belarus in what the EU called an orchestrated effort by the authorities in Minsk.
Frontex has been helping Lithuania handle migration from Belarus, and the agency's fundamental rights officer has logged at least 20 violations of migrant rights at hands of Lithuanian border guard by October, according to an EU Observer report.
"We are trained to comply with the fundamental rights, we are aware that there is the right to have international protection, but on the other hand there are illegal behaviors and illegal crossing that are not in line with EU regulation," Leggeri added.