Policymakers in the single currency area were at loggerheads on Tuesday over the long-term implications of the Cyprus bailout and whether savers across Europe will be exposed to raids on their bank accounts in future rescues.

The European commission and influential MEPs involved in drafting new laws on resolving bank failures confirmed that the proposed rules would include "bail-ins", which are favoured by Germany and would see investors and savers taking the hit instead of taxpayers.

But eurozone central bankers contradicted the signals from Brussels, insisting that the formula agreed for Cyprus on Sunday would not be applied uniformly in banking crises in other countries. Slovenia may be the first to find out as anxiety mounts that the country faces a worsening bank crisis that may necessitate eurozone intervention within months.

Cyprus's central bank, meanwhile, announced that savers with more than €100,000 (£85,000) in Bank of Cyprus, the island's biggest lender, would lose 40% of their savings as part of the radical restructuring and downsizing plan agreed by President Nicos Anastasiades and eurozone leaders in Brussels on Sunday. The losses to savers comes on top of the wipe-out of €4.2bn of deposits at Laiki or Cyprus Popular, the country's second bank which is being closed down and its good assets transferred to Bank of Cyprus.

The controversy over having savers and investors foot the bill for bank failure erupted on Monday when Jeroen Dijsselbloem, the inexperienced Dutch finance minister who has been chairing the eurogroup committee of finance ministers for two months, said that the Cyprus model would be extended to other countries and situations to avoid the injustice of having taxpayers shell out for the risky behaviour of bankers.

His remarks bore the hallmarks of policies pursued in particular by Berlin since last year. But the timing of his remarks were viewed as a disastrous gaffe as the markets plunged and speculation mounted about deposits fleeing the eurozone periphery for the safer havens of northern Europe.

"It is not excluded that deposits over €100,000 could be instruments eligible for bail-in," said Chantal Hughes, spokeswoman for Michel Barnier, the European commissioner for the single market drafting the banking resolution legislation. Gunnar Hökmark, an MEP involved in steering the legislation through the European parliament, said the chamber would insist on having savers contribute to future bank rescues. "Deposits below €100,000 are protected … Deposits above €100,000 are not protected and shall be treated as part of the capital that can be bailed in," he told Reuters.

In June last year, an EU summit for the first time agreed that the eurozone's bailout fund, the European Stability Mechanism, could be used directly to recapitalise ailing banks without the loans being added to government debt. It was a breakthrough engineered by France, Italy, and Spain but opposed by Germany, which has since sought to neuter the idea. Following the Cyprus deal, where none of the €10bn in bailout funds will be used to recapitalise banks, the idea is viewed as dead.

But Dijsselbloem's remarks, which he sought later to retract and qualify, merely compounding the panic, were dismissed on Tuesday in various capitals and by the European Central Bank. Benoît Coeuré, a French member of the ECB executive, said: "Dijsselbloem was wrong to say what he said. The experience of Cyprus isn't a model for the rest of the eurozone … No country has the same concentration of problems as Cyprus." Austria's central banker, Ewald Nowotny, added: "Cyprus is a special case."