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The parliament did not give the lawmakers' names but said it was in response to an investigation by Belgian law enforcement into the graft allegations.
Sources briefed on the Belgian probe told AFP the two MEPs targeted by the procedure were an Italian, Andrea Cozzolino, and a Belgian, Marc Tarabella.
Both are members of the centre-left Social and Democrats grouping in the parliament.
The development follows a string of Belgian police raids in December on the addresses of MEPs, former MEPs and lobbyists that turned up a total 1.5 million euros ($1.6 million) in cash.
There are suspicions that the money was tied to alleged graft in the European Parliament benefiting Qatar.
Qatar denies having a role in any wrongdoing.
The scandal has shaken the European Parliament, with one of Metsola's vice presidents, Greek MEP Eva Kaili, among four suspects arrested in the raids in Belgium.
Through her lawyer, Kaili has denied knowing of the existence of 150,000 euros found in her home and asserted she is innocent.
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A Belgian judge determined that parliamentary immunity did not apply in Kaili's case because she was allegedly caught red-handed. She remains in custody.
Tarabella's home was searched by Belgian authorities on December 10, according to a law enforcement source.
Metsola, tweeting about her procedure to lift the two MEPs' immunity, said: "There will be no impunity. None."
The parliamentary speaker has sought to frame the scandal as an outside attack on European democracy.
She has also vowed reforms to clean up the parliament, including by strengthening whistle-blower protections, banning all "unofficial friendship groups" with foreign governments, and increasing vetting of MEPs finances.
(AFP)