Roberta Metsola has warned members of the European Parliament that alleged corruption by Qatar was an attack on democracy after investigators arrested one of her deputies.
"Make no mistake," the EP president said. "The European Parliament, dear colleagues, is under attack. European democracy is under attack and our free and democratic societies are under attack."
Metsola, who this weekend attended a police search of an MEP's home, addressed the crisis during the opening of the plenary session in Strasbourg on Monday afternoon.
The allegations that Qatar bribed EU officials to try to win influence have rocked the European institutions.
Her comments came as news emerged that Belgian graft investigators had searched EU parliament offices over the corruption allegations.
Belgian police have so far arrested four people, including Greek MEP Eva Kalli, one of the 14 vice presidents of the EP. Bags of cash were found in her home shortly after she returned from an official visit to Qatar.
The four have been charged with corruption and money-laundering. Qatar, which is currently hosting the World Cup, has denied any wrongdoing.
Metsola suspended Kalli from her role and told parliament she had convened a meeting of the Conference of Presidents to bring her term as vice-president to an end.
The Nationalist Party MEP, who accompanied a Belgian judge and police to a house search last weekend, promised to act "in sync with authorities", allowing IT equipment to be secured and offices sealed.
Metsola, elected to lead the European Parliament in January, told MEPs that the last few days had been the "longest" of her career.
"If my fury, my anger, my sorrow do not come across please be assured that they are very much present," she told her colleagues, "along with my determination for this House to grow stronger".
She said that "malign actors, linked to autocratic third countries" have allegedly "weaponised NGOS, Unions, individuals, assistants and MEPS to subdue our processes".
But she said their "malicious plans" would fail.
She said she had also paused the progress of a report allowing an EU visa waiver for Qatar.
It is one of the largest corruption scandals to ever hit the European Parliament and a huge test of Metsola's presidency.
"There will be no sweeping under the carpet", she told MEPs, vowing to launch an internal investigation, a process of reform and to strengthen the protection of whistleblowers. "We will shake up this Parliament and this town and I need your help to do it", she vowed.
"But I must also say that while we can always look to increase deterrents and transparency, there will always be some for whom a bag of cash is always worth the risk," she said in an apparent reference to the money seized at Kalli's home.
"To those malign actors, in third countries, who think they can buy their way forward, who think Europe is for sale... Let me say that you will find this Parliament firmly in your way. We are Europeans. We would rather be cold than bought," she concluded.