The bloc´s executive body is planning a sanction of €250,000 (£200,000; $290,000) for every refugee refused entry by member states. But the proposals were rejected almost immediately by right-wing governments in Poland and Slovakia, with the latter´s foreign minister saying the proposal "sets us back nine months and does not respect the reality".
The Commission wants changes made to an asylum system which has buckled amid an influx of migrants. The plans would require support from most member states as well as MEPs.
EU officials hope that, twinned with a deal with Turkey that has already reduced migrant numbers, tensions over migration within the bloc can be reduced.
The basic Dublin regulation would be kept, requiring refugees to claim asylum in the member state in which they arrive.
However, there would be several changes, including plans to help countries receiving "disproportionate numbers" of asylum claims.
The EU already has a flagship scheme to redistribute 160,000 migrants around the continent, but it has met only a tiny fraction of this target since it was agreed in 2015.
The planned figure of €250,000 per refused claimant could be revised but the Commission is known to want a punitive level.
The UK and Ireland can opt out of asylum policies, and the British government has already indicated it will not take part. Denmark is also exempt.
Under the fresh proposals, if a country receives more than 150% of its annual "fair share" of asylum seekers, the relocation scheme would kick in. That share is calculated according to a country´s population and economy
"There´s simply no way around it: whenever a member state is overwhelmed, there must be solidarity and a fair sharing of responsibility within the EU," Commission Vice-President Frans Timmermans said.
Countries refusing to accept their quota would effectively be fined - with the money going to frontline states such as Italy and Greece that have carried the burden.
The proposals for sanctions alarmed Central European countries that have refused to implement the refugee quota deal. One senior Polish official said last week that the plan was dead.
Hungary, Romania, the Czech Republic and Slovakia were outvoted when the quota plan was agreed. Poland had agreed to take some 7,000 asylum seekers and could face a fine of at least €1.75bn if the proposal goes through.
The government in Budapest on Tuesday announced plans for a referendum on the EU´s resettlement plans.