MEPs on Wednesday refused to approve the budget for the bloc's border agency, demanding to see a report into alleged human rights violations against migrants.
The vote in parliament came less than a week after Fabrice Leggeri stepped down as Frontex chief following the release of a media investigation into alleged misconduct and human rights violations by Frontex staff including migrant push-backs.
Their report stated that Frontex recorded at least 22 pushbacks in the Aegean Sea between March 2020 and September 2021 as "prevention of departure".
A year-long investigation by the EU's anti-fraud office, OLAF, into these claims was also concluded in February.
MEPs in Strasbourg voted to withhold their approval of Frontex's 2020 accounts by 492 votes in favour, 145 against and eight abstentions. They said in a statement that approval with be withheld "until full OLAF investigation report becomes available".
They also said the agency has failed to fulfil the conditions set out by MEPs in their previous discharge report which included the recruitment of 20 fundamental rights monitors and three deputy executive directors as well as the creation of a mechanism to report serious incidents on the EU’s external borders and a functioning fundamental rights monitoring system.
Ahead of the vote, Czech MEP Tomáš Zdechovský (EPP), stressed that "Frontex operates in challenging circumstances and with its enhanced role comes the need for effective management and greater accountability".
"Though the Agency has made progress in the last year, we currently do not have enough information to make a well-informed decision to grant discharge. We, therefore, postpone this decision to autumn 2022."
Belgian MEP Saskia Bricmont (Greens/EFA) meanwhile said that Leggeri's resignation "doesn't address structural problems" at the agency.
Frontex's Executive Management, which will helm the agency until a replacement for Leggeri is found, praised its staff earlier this week for responding to the refugee influx from Ukraine "rapidly and professionally."
"In these turbulent times Europe needs the European Border and Coast guard Agency, it needs us, and we must be strong and resilient. As a civil service our job is to comply with legislation, live up to expectations and to uphold European Union values.
"Protecting the security of the EU's external borders and protecting the fundamental rights of those crossing them is no contradiction, upholding fundamental rights is a defining value, woven into the fabric of our identity. Let us together shape the Agency as a role model of border service professionalism under rule of law," they added.