Most of the fraudulent subsidies went to the island of Crete, where the family of Prime Minister Kyriakos Mitsotakis has been politically influential for over a century.
Three Greek cabinet members resigned on Friday in a burgeoning EU farm subsidy scandal that has heaped pressure on the country's conservative government, state TV ERT reported.
The channel said the ministers of agriculture and civil protection had resigned, alongside a deputy health minister, with the government spokesperson set to make announcements on a reshuffle.
It comes after it emerged on Thursday that European prosecutors were probing an increasing number of Greece's ruling party politicians for potentially skimming EU farm subsidies, widening an almost year-long scandal that has heaped pressure on the government.
The EU's European Public Prosecutor's Office (EPPO) first detailed the scam last May, accusing subsidy beneficiaries of making claims for land that they did not own and exaggerating the number of animals on farms.
Some people receiving payments had no link to agriculture.
The allegations led to a string of raids and arrests last October, as well as long-running protests from farmers who had their legitimate subsidies held up.
Politicians belonging to the New Democracy ruling party have been increasingly ensnared in a scandal potentially involved tens of millions in subsidies, with the EPPO now probing 20 of them.
The prosectors demanded on Wednesday that 11 MPs should have their immunity from prosecution lifted, and detailed seven more politicians they suspected of involvement, reportedly including a former agriculture minister.
The agency said on Thursday there were another two MPs under suspicion, confirming a report by state news agency ANA.
"I can confirm that," said Tine Hollevoet, spokesperson for the office based in Luxembourg. "However, I will not confirm any names."
Most of the fraudulent subsidies went to the island of Crete, where the family of Prime Minister Kyriakos Mitsotakis has been politically influential for over a century.
Opposition parties have called for the resignation of any ministers under investigation.
Mitsotakis, who has stressed that the fraud began before he came to power in 2019, has vowed to imprison the "thieves" responsible and to reclaim the funds.
Elections are scheduled next year and Mitsotakis's conservative party leads in opinion polls, but is not expected to secure an absolute majority.