APA is a key institution in ensuring the stability and development of agriculture, as it manages substantial financial resources from both European and national funds, serving as the primary source of funding for Slovak farmers and municipalities. The agency allocates hundreds of millions of euros in national funds, with its budget exceeding one billion euros with European financial assistance. State auditors recently examined selected calls for proposals from 2020 to 2024, representing nearly 272 million euros in disbursed funds. Eligible expenses paid out amounted to over 83 million euros. Of the two main areas of APA's support, the SAO audit focused on project-based funding, with documentation scrutinized for vulnerability to corruption risks.

The audit identified deficiencies such as inconsistencies in application processing, incomplete documentation, and insufficient professional training of some employees. These findings indicate that failures primarily occur in practice rather than the system’s design. "According to international standards and in line with the Slovak government's anti-corruption policy, even a single case of misconduct or rule violation is enough to conclude that the system does not provide sufficient protection against corruption and fraud risks and may be deemed ineffective. Further findings from the auditors revealed risks associated with failures in prevention and risk management within the agency," explained the president of the Supreme Audit Office, Ľubomír Andrassy.

Additional risks to fair and transparent decision-making stem from high staff turnover and inadequate professional qualifications. Auditors discovered significant personnel changes at APA, with three changes in general directors during the audit period and ten reorganizations since 2020. Within the project support division alone, eight directors have been replaced. The agency’s employees, who evaluate funding applications, play a crucial role. However, APA has long lacked fixed requirements for minimum professional education or experience and does not have effective mechanisms to prevent conflicts of interest. As a result, an evaluator could be, for example, a receptionist without relevant training or experience. Bureaucracy and a weak ethical culture further exacerbate corruption risks.

The process of assessing non-repayable financial contributions is affected by severe delays. The SAO audit revealed that one funding request was denied approximately 1,280 days after submission, despite decisions in that particular call being required within 300 working days. Another applicant received a decision only after eight years when APA ultimately withdrew from the contract. Such delays reduce process predictability, complicate project management, and undermine trust in the system. Ambiguous conditions, unclear rules, and inconsistent penalties for applicant errors increase administrative burdens and raise concerns about equal treatment. The national authority for external control found that in one case, no penalty was imposed despite extensive ineligible expenditures being identified. In another, under similar circumstances, sanctions were properly applied. This inconsistent approach threatens equal treatment and creates opportunities for fraud and corruption.

Administrative financial controls revealed a lack of a clear, automated, and transparent system for assigning auditors or evaluators, leaving room for subjective decision-making and potential manipulation. On-site financial audits exposed violations of fundamental principles, such as proper auditor rotation and the clear delegation of responsibilities between supervisors and auditors, creating additional opportunities for corruption. This risk is compounded by the fact that auditors did not receive clear assurances during their investigation that every audit conducted by APA employees was properly documented and archived.

Although APA is taking steps to improve electronic support and enhance transparency, these reforms must be thorough, sustainable, continuously monitored, evaluated, and effectively implemented. Despite recent improvements to the agency’s information system, it still exhibits issues, including the ability to manually alter finalized documents, which could lead to data manipulation. "If APA fails to demonstrate a commitment to continuing reforms, it risks losing public trust and facing increased scrutiny from oversight institutions. Maintaining accreditation depends on strict adherence to regulations, risk assessments, and professionalization—critical for ensuring fair and transparent funding distribution," stated SAO President Ľ. Andrassy. A positive sign is that even before the audit report was finalized, the agency had already adopted 19 corrective measures to address deficiencies identified by the audit office.