Replacements for all five will be named "in the coming days," government spokesman Pavlos Marinakis said in a statement.
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Five high-ranking Greek government officials, including a minister and three deputies, resigned on Friday following allegations of involvement in corruption over the mismanagement of European Union farming subsidies.
The case stems from the alleged mismanagement of EU subsidies for agriculture between 2019 and 2022 by a government agency, known by its Greek acronym OPEKEPE, tasked with handling the funds.
According to the European Public Prosecutor's Office, a "significant number of individuals" received subsidies through the agency based on false declarations, including claims of owning or leasing pastures that were in fact public land.
The suspects continued submitting false declarations of livestock until 2024, maintaining subsidy payment entitlement, it added.
The prosecutor's office sent a hefty case file to Greece's parliament earlier this week including allegations of the possible involvement of government ministers in an organised fraud scheme.
Members of parliament enjoy immunity from prosecution in Greece that can only be lifted by parliamentary vote.
In a resignation letter to the prime minister on Friday, Migration and Asylum Minister Makis Voridis maintained his innocence, saying he was stepping down in order to concentrate on clearing his name.
Voridis served as agriculture minister from mid-2019 to early 2021.
Prime Minister Kyriakos Mitsotakis accepted his resignation, as well as those of the deputy ministers of foreign affairs, agriculture and food, and digital governance, and of the general secretary of agriculture and food.
Replacements for all five will be named "in the coming days," government spokesman Pavlos Marinakis said in a statement.
The European Commission announced earlier this month it would reduce the amount of farm subsidies for Greece by 5%, for a total of €392 million.