The European Public Prosecutor’s Office is examining whether European Union funds were improperly paid to businesses within the Agrofert conglomerate and whether Czech authorities failed to recover subsidies awarded during Babiš’s earlier term as prime minister from 2017 to 2021.
Czech police have been asked to assist the inquiry. A prosecutor authorised the opening of criminal proceedings on May 24 after reviewing information relating to subsidy approvals and payments. The investigation does not establish wrongdoing and may conclude without charges.
The case is understood to cover current payments as well as roughly €300 million in subsidies that critics argue should have been reclaimed. Agrofert companies receive agricultural support and funding for investment and innovation projects across a business network that includes farming, food production, chemicals and media-related interests.
Babiš, 71, has denied breaching conflict-of-interest rules. He says his transfer of Agrofert into an independently managed trust placed the conglomerate beyond his ownership and control, meeting standards required under Czech and EU law.
Finance Minister Alena Schillerová has defended the arrangement, saying the prime minister addressed the conflict-of-interest issue. The government has not indicated that it expects the investigation to affect subsidy administration or Babiš’s position.
Opposition parties dispute that assessment. They have questioned whether the trust provides sufficient separation between Babiš and the conglomerate, particularly because reported provisions could allow members of his family to regain control after he leaves public office.
The Pirate Party said the proceedings followed a complaint it submitted over earlier subsidy payments. Its petition raised questions about officials and politicians who authorised funds despite continuing uncertainty over Agrofert’s beneficial ownership and Babiš’s potential financial interest.
The European Commission has separately sought detailed information from Prague about the trust structure and other assets linked to the prime minister. Czech explanations supplied earlier this year did not resolve all the questions raised by EU officials.
The Commission has also examined whether businesses outside the Agrofert trust, including investment interests connected to fertility clinics, could benefit from EU financing. Czech authorities have been advised to exercise caution when requesting reimbursement from the EU budget for subsidies involving entities linked to Babiš.
The dispute carries a potential cost for Czech taxpayers. If Brussels decides that payments were incompatible with conflict-of-interest safeguards, the national government could be required to finance the subsidies itself or seek repayment from recipient companies.
Agrofert was placed in trust after Babiš returned to government following the 2025 parliamentary election. His ANO movement emerged as the largest political force and formed a coalition that has challenged several mainstream EU policies, including the scale of support for Ukraine.
The subsidy investigation is separate from the long-running Stork’s Nest case, which concerns about €2 million in EU funding intended for small and medium-sized businesses. Prosecutors alleged that a farm and conference centre was temporarily separated from Agrofert and transferred to Babiš’s relatives to qualify for assistance.
Babiš was acquitted twice in that case, but both rulings were overturned on appeal. Czech lawmakers voted in March against lifting his parliamentary immunity, preventing the court from continuing proceedings against him while he remains an MP. A trial could resume after his parliamentary mandate ends.
Jana Nagyová, a former Babiš associate and now a member of the European Parliament, was given a three-year suspended sentence and a fine in May over her role in obtaining the Stork’s Nest subsidy. She has the right to appeal.
The wider conflict-of-interest dispute dates back to Babiš’s first premiership. EU audits concluded that placing Agrofert in trust did not necessarily eliminate his economic interest because he remained a potential beneficiary and retained influence over the arrangement.
Those findings led to restrictions on reimbursements and legal disputes over whether Agrofert projects qualified for EU support. The latest investigation shifts the issue from administrative auditing towards possible criminal responsibility for decisions concerning the European budget.
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