Giovanni Kessler, a former Italian MP and anti-mafia prosecutor, is suspected by Belgian authorities of illegally listening in to a phone conversation during his effort to unearth evidence in a corruption case involving the EU, known as Dalligate.
EU health commissioner John Dalli of Malta was forced to resign four years ago after a probe led by Kessler linked him to a tobacco lobbyist at a time when the EU was introducing tougher anti-smoking legislation.
"His immunity was lifted by the European Commission," Eric Van der Sypt, a spokesman for the federal prosecutor's office told AFP.
Many EU civil servants in Belgium are granted diplomatic immunity, in addition to paying no taxes in the country.
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The European Anti-Fraud Office, known as OLAF, said with his immunity lifted, Kessler now had the option to bring legal action against the commission before the European Court of Justice "in order to protect OLAF's independence".
Belgian authorities first demanded the Commission lift Kessler's immunity in December 2014, triggering accusations that the commission was trying to delay the case.