The European Parliament on Tuesday refused to approve Frontex's 2020 accounts in the wake of claims of human rights abuse under its previous leadership.
Frontex is the EU agency with the biggest budget, totalling €754 million this year.
MEPs in Strasbourg on Tuesday voted against the border agency's discharge with a 345 to 284 votes margin.
The vote is largely symbolic and should not result in any penalty for Frontex.
It was a protest vote over the agency's previous management under Fabrice Leggeri, who stepped down in April following an investigation by the bloc's anti-fraud office.
Complicit in pushbacks
An OLAF probe reportedly found that Frontex was complicit in illegal pushbacks of migrants by the Greek coast guard in 2020 and 2021.
The parliament said in a statement the vote was criticism of the "magnitude of the committed serious misconduct".
It said "the agency failed to protect the fundamental rights of migrants and asylum seekers and, according to media reports, was involved in the illegal pushbacks of at least 957 refugees between March 2020 and September 2021".
MEPs also expressed shock over the suicide of a staff member, “related to alleged practices of sexual harassment” and noted that 17 cases of sexual harassment in the agency were reported in 2020, of which 15 were closed without a follow-up.
Greens push for prosecutions
Green MEPs welcomed the vote, tweeting: "No EU money should fund human rights violations. MEPs just decided not to accept the 2020 budget by Frontex due to its continuous involvement in pushbacks."
Separately, they are urging people to join its call on the European Commission to halt funding to countries performing pushbacks - including Malta - and take them to the EU Court of Justice.
"Tens of thousands asylum seekers have been brutally pushed back at Europe’s borders in the past years. Sometimes even with the help of Europe’s border agency Frontex.
"These illegal actions of EU countries such as Croatia, Greece, Hungary, Italy, Lithuania, Malta, Poland, Slovenia and Spain involve threats, physical violence, assault and abuse during detention or transportation," it is claiming.
The S&D similarly flagged concern over "too many worrying allegations of illegal pushbacks of migrants" at borders.
Too many problems remain unsolved in Frontex, it said, adding in a Tweet that "too little has been done for us to grant discharge for 2020 accounts. We call on Frontex to change its culture of mismanagement and cover-up".
A woman holds her child's head following a Frontex rescue operation on the island of Lesbos in Greece in 2020. Photo: AFPEPP sticks up for Frontex
The EPP, however, slammed the vote.
"We fully support the important job that Frontex is doing in protecting our external borders," it tweeted.
"Refusing to grant discharge undermines this important mission, which must remain robust and efficient, with respect for fundamental rights."
This was not the field for political games, it said, adding that weakening Frontex translated into weakening of border protection.