Manfred Weber, head of the centre-right European People’s Party, argued his case on Tuesday, amid concerns anti-EU candidates in both the Netherlands and France could make large gains in elections over the coming weeks.
The German politician said: “The question is whether Europe is stupid enough to fund its enemies.”
Mr Weber, who is affiliated with Angela Merkel's ruling Christian Democratic Union party, told AFP he sent his proposal for new legislation in a letter to European Commission head Jean-Claude Juncker.
The details would be hammered out over the next couple of months, Mr Weber said.
Eurosceptic parties expressed anger at the proposal, which is part of a revamp launched last year on how European parties are funded.
“Raging Europhiles such as Weber have lost the argument and popular support and in their despair now wish to utilise finance as a weapon to hamper patriotic parties,” said current Ukip leader and MEP Paul Nuttall.
“There is no such thing as EU money, it's taxpayers' money and Eurosceptic parties have a mandate from their voters who pay tax,” he said.
UKIP and France's Front National, headed by presidential candidate Marine Le Pen, have been accused in the past of siphoning off EU funding to pay for national campaigning.
Ms Le Pen has refused to repay nearly 300,000 euros (£262,000) in EU funds that the European parliament, which is based in both Strasbourg and Brussels, said were paid illegally to a party assistant in Paris.
MEPs will hold a debate on the topic of removing funding from some parties during a plenary session in Strasbourg on Wednesday.
“What we are concerned with right now are the basic principles: we have got parties hostile to Europe that are enjoying European funding,” Mr Weber said.