The EU’s former chief diplomat Federica Mogherini and two other people have been formally accused of fraud and corruption, the European prosecutor’s office has said.

The European Public Prosecutor’s Office (EPPO) did not refer to Mogherini by name, but said the rector of the College of Europe in Bruges – her role – had been formally notified of the accusations. A senior staff member of the college and a senior official from the European Commission were also indicted, the EPPO said, after all three were questioned by Belgian police.

The investigation, which led to police raids on the headquarters of the EU foreign service in Brussels and the elite College of Europe postgraduate school, as well as Mogherini’s home, has deeply shocked EU insiders. Prosecutors suspect fraud in the tender for a contract to run a training academy for young diplomats, which was awarded to the College of Europe by the EU foreign service.

The EPPO, the EU agency in charge of prosecuting fraud involving European funds, said the accusations concerned “procurement fraud, corruption, conflict of interest and violation of professional secrecy”. It added: “All persons are presumed innocent until proven guilty by the competent Belgian courts of law.”

All three have been released “as they are not considered a flight risk”, the EPPO said.

On Wednesday, Mogherini issued a statement via the College of Europe. “In its long tradition, the College has always applied and will continue to apply the highest standards of integrity and fairness,” she said. “I have full confidence in the justice system and I trust that the correctness of the College’s actions will be ascertained.”

The College of Europe has said it would cooperate fully with the authorities “in the interest of transparency and respect for the investigative process”.

In a letter to staff seen by the Guardian, the EU’s current foreign policy chief, Kaja Kallas, said the allegations were “deeply shocking but should in no way tarnish the good work that the vast majority of you are doing every day”.

Kallas, who is one year into a five year mandate, said integrity and accountability “will only improve under my watch” and that the current process showed “safeguards are in place and working”.

One of the accused is understood to be Stefano Sannino, a senior commission official, who was secretary general of the European External Action Service from 2021 to 2024. A request for comment sent to him was referred to the commission, which declined beyond saying it was co-operating with an investigation into activities that took place before the term of the current EU foreign policy chief, Kaja Kallas.

Mogherini was the EU’s high representative for foreign affairs from 2014 to 2019, after a brief stint as Italy’s foreign minister. She went on to become rector of the College of Europe, a training ground for European officials and politicians. Her appointment in 2020 proved controversial, with some alumni arguing she lacked academic credentials and experience of running a major academic institution.

The College of Europe, which receives EU funding, was awarded the tender in 2020-21 to run the European Union Diplomatic Academy, a nine-month training programme for young diplomats. Prosecutors have said they have strong suspicions that confidential information had been shared with one of the candidates taking part in the process.

The diplomatic academy was launched as a pilot project in 2022 with a budget of nearly €1m (£880,000) and the aim of “building a European diplomatic corps that shares a truly common diplomatic culture”, according to the commission website. Mogherini, who also serves as director of the academy, described it as “a great step forward” for European diplomacy.

About 40 diplomats from EU member states and institutions took part in the first nine-month programme in 2022-23, with 50 joining in the second year. In the second programme, diplomats spent four months in Bruges and a month at the EEAS headquarters in Brussels, as part of the programme where they were trained in EU policies, as well as diplomatic skills such as negotiation, communication and protocol.