The shock idea comes as anti-EU candidates in the Netherlands and France are expected to make inroads in elections over the coming weeks.
Many of these parties, including the pro-Brexit UKIP formerly headed by Nigel Farage, have a considerable presence in European Parliament, which has become a crucial source for funding.
"The question is whether Europe is stupid enough to fund its enemies," said Manfred Weber, head of the centre-right European People's Party, the biggest in the European Parliament.
Weber, who is affiliated to Angela Merkel's ruling CDU party in Germany, said 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, Weber said.
Europseptic parties bristled 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.
Opposed to a united Europe, major eurosceptic parties have had success winning seats in European Parliament and securing the EU funding that comes with that.
UKIP and France's Front National, headed by presidential candidate Marine Le Pen, have been targeted for allegedly siphoning off EU funding to pay for national campaigning.
Le Pen has refused to repay nearly 300,000 euros ($325,000) 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 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." Weber said.
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