EU member states may have already set up rules to protect citizens' deposits, but as euro zone lenders have struggled to combat the banking crisis -- together with the Greek capital controls over the summer -- the Commission is suggesting measures are bolstered.
"The point of this proposal is to make sure that people's deposits up to the guaranteed amount of 100,000 euros are really safe, without people having to worry on financial situation in the given member state," the European Commission's vice president Valdis Dombrovskis told CNBC.
"Meaning if some of the member states are not able to fulfil its obligations, it is facing a banking crisis, there will be a European back-stop," he said.
According to the EU leaders' report, banks would fund the European scheme and the proposal, which will need to be passed by individual member states for it to become EU member law.
Germany has strongly opposed the so-called "risk-sharing" measures, as money used to guarantee German deposits could be used to bailout savers elsewhere in Europe.
"As regards Germany, of course there is some criticism in our proposal we are looking at some of the concerns raised. And first the concern is having a level playing field," Dombrovskis said.
"Of course our proposal will take into account different starting levels. It cannot end up as a situation where those member states that have fully funded deposit guarantee schemes who pay for those that do not," he said.
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Reuters contributed to this report.