Allegations Qatar bribed EU officials to try to win influence are of the “utmost concern”, European Commission President Ursula von der Leyen says.
Ms von der Leyen said the accusations were “very serious” and called for the creation of a new EU ethics body.
Belgian police have arrested four people, among them European Parliament Vice-President Eva Kaili.
The four have been charged with corruption and money-laundering. Qatar has denied wrongdoing.
The BBC’s Brussels correspondent, Jessica Parker, says details released by Belgian authorities in the last few days left many people’s jaws on the floor.
MEPs who spoke to our correspondent say they are shocked by both the scale and blatancy of the accusations.
Belgian police seized cash worth about €600,000 ($632,000; £515,000) in 16 searches in Brussels on Friday. Computers and mobile phones were also taken.
No suspects have been publicly named, but Ms Kaili is understood to be among those who have been indicted.
Ms Kaili – an MEP for eight years – was suspended from her duties as one of 14 vice-presidents by the president of the European Parliament, Roberta Metsola.
She has also been suspended from the parliament’s Socialists and Democrats Group and expelled from the Greek centre-left Pasok party.
Prosecutors in Greece have reportedly frozen all of Ms Kaili’s assets.
Watchdogs and opposition MEPs said the bribery investigation could represent one of the biggest corruption scandals in European Parliament history.
Ms von der Leyen said confidence in European institutions required the highest ethical standards.
“The allegations against the vice-president of the European Parliament are of utmost concern, very serious,” she said.
“It is a question of confidence of people into our institutions, and this confidence of trust into our institutions needs higher standards.”
Hungarian Prime Minister Viktor Orban mocked the EU after the allegations surfaced.
Tweeting a photo of former US presidents Ronald Reagan and George HW Bush that is often used as a meme, he referred to the European Commission’s recommendation to freeze billions of euros in funds earmarked for Hungary.
Prosecutors said they suspected a Gulf state had been influencing economic and political decisions of the parliament for several months, especially by targeting aides.
Local media has named the state as Qatar, although the Qatari government said any claims of misconduct were “gravely misinformed”.
Ms Kaili’s responsibilities as vice-president include the Middle East. She has been a defender of Qatar in the past.
The European Parliament is the EU’s only directly elected institution. Some 705 members of parliament, elected by voters in the 27 nations which make up the EU, meet to scrutinise proposed legislation and vote through European law.__Courtesy BBC