The European parliament has formally censured the Czech prime minister, Andrej Babiš, over conflict of interest accusations, in unprecedented criticism of a serving leader.

MEPs called for the suspension of all EU payments to a business owned by the billionaire PM in a non-binding resolution adopted by 434 votes to 64, with 47 abstentions.

The move will pile pressure on Babiš, who has been accused of a conflict of interest over his role as prime minister and links to Agrofert, the food, chemicals and agriculture conglomerate he founded.

Thousands of protesters in Prague called on the tycoon-turned-politician to resign last month over separate corruption allegations. The Czech leader’s son recently said he had been lured to Crimea and abducted to stop him testifying about his father’s business interests.

Voting in Strasbourg, MEPs said all funds paid “illegally or irregularly” should be recovered and called for a full and transparent investigation to resolve the conflict of interest.

Speaking before the vote, Babiš said he had always acted within Czech law.

The parliament also called on EU leaders and ministers to take action to prevent conflicts of interest when drawing up rules for the next long-term EU budget.

“Business and politics is a delicate combination that should not leave any doubts for a conflict of interest,” said Ingeborg Grässle, a German MEP who chairs the parliament’s budget control committee and co-authored the resolution. Babiš’s role as the head of the Czech government, with his business, “obviously create this conflict”, she said.

EU lawyers concluded that Babiš was in a conflict of interest in a confidential legal opinion seen by the Guardian last month, and which MEPs cited in the resolution.

MEPs voiced regret that the European commission, which controls EU funds, had remained passive despite “strong indications” of a conflict of interest when Babiš became Czech finance minister in 2014.

Babiš, the second richest man in the Czech Republic, has always denied any conflict of interest, and says Agrofert is in a blind trust he does not control. Agrofert also rejects the claims.

“For me, this is a political affair. I am convinced it will be shown that I do not have any conflict of interest,” Babiš said on Czech Television before the vote.

Parliament sources are unable to recall such formal censure of a serving EU leader. MEPs raised concerns about corruption and conflicts of interest in Hungary in a September vote, but avoided naming names. The text referred to “the prime minister’s son-in-law”, a reference to an investigation by the EU’s anti-fraud office into street lighting contracts awarded to István Tiborcz, who is married to the daughter of Viktor Orbán.

Philippe Lamberts, the co-leader of the Greens, which initiated the resolution, said the commission had to act to resolve the issue. “The Czech authorities cannot be expected to effectively rule against their own prime minister,” he said. “EU money is taxpayers’ money and we cannot let it be funnelled off by the rich and powerful.”