Fabrice Leggeri's resignation comes a day after an investigative report said the EU border agency had illegally forced back nearly 1,000 asylum seekers in the Aegean Sea.
The head of the European Union's border agency confirmed he is stepping down on Friday following reports of misconduct and human rights violations toward migrants.
"I give my mandate back to the Management Board as it seems that Frontex mandate on which I have been elected and renewed in June 2019 has silently but effectively been changed," Fabrice Leggeri wrote in a statement, relayed by multiple media.
An EU spokesperson denied however that the agency's mandate had changed.
"Frontex has a critically important task which is to help member states to protect the common EU external border and to uphold at the same time fundamental rights in doing so," said Anitta Hipper, Spokesperson of the European Commission for Home Affairs, Migration and Internal security.
Leggeri was appointed to helm Frontex in 2015 as the bloc was dealing with an influx of migrants. The agency has come under criticism over the past couple of years over alleged pushbacks — the illegal practice of forcing back migrants who have reached EU territory, whether on land or at sea.
His resignation comes a day after a report was released by a consortium of European media organisations including France's Le Monde, Germany's Der Spiegel, Switzerland's SRF et Republik, and the investigative journalism NGO Lighthouse Reports, which found that Frontex recorded at least 22 pushbacks as "prevention of departure".
These involved more than 950 migrants and were reportedly carried out between March 2020 and September 2021 by Frontex and the Greek authorities in the Aegean Sea.
The EU's anti-fraud watchdog, OLAF, investigated the reports for over a year and is due to release its report soon. Its chief, Ville Itälä, presented some of their findings to the European Parliament's Committee on Civil Liberties, Justice and Home Affairs in late February.
"According to the summary, the report — which MEPs do not have access to — reveals that Frontex's management was aware of human rights violations and deliberately avoided reporting them; up until now, they have denied any wrongdoing, pointing instead to supposed ambiguities in EU regulations," Green MEP Erik Marquardt wrote in a letter to the Commission demanding what action would be taken against Frontex's management.
Human rights NGOs have meanwhile recorded other instances of pushbacks in Poland, along the border with Belarus, as well as in Spain and Croatia.
The European parliament's Left group has called for a debate on Frontex and its mandate to be held next week during plenary sessions in light of Leggeri's resignation and allegations of human rights violations.
"Leggeri personally had an active role in Frontex’s complicity in fundamental rights violations and the cover-up of this complicity included lying to the Parliament more than once. We have been calling for his resignation for years. It was overdue," German MEP Cornelia Ernst (Die Linke) said in a statement.
"Leggeri’s actions reveal once again the serious structural problems with the EU border agency, which need to be tackled. Frontex involvement in human rights violations will not stop just because Leggeri is gone. Now is the time to go further. Frontex must immediately suspend its operations in Greece in accordance with Article 46 of the Frontex Regulation," she added.