Migration Commissioner Dimitris Avramopoulos said member states had until September to take in 160,000 Syrian and other refugees from the two countries, which have been on the frontline of the migration crisis.
So far only 13,500 have been relocated in a process bogged down by general inertia and resistance from Eastern European states which oppose Muslim immigration.
"If we don't have tangible efforts by September...The commission will not hesitate to make use of its power," Avramopoulos, who is Greece's EU commissioner, told a news conference.
"But if it is not the case in the future, infringements might be an option," he said.
As the executive branch of the 28-nation EU, the European Commission is able to launch "infringement proceedings" to impose fines on member state that break the bloc's rules.
Countries like Hungary and Slovakia have proposed paying "solidarity" contributions instead of actually taking in any migrants.
But others such as France and Germany insist that no country can shirk its duty to admit a minimum number of refugees under the plan, which was pushed through in September 2015.
In February, EU vice president Frans Timmermans said the Commission was for the first time considering penalties for states that break the rules.
Meanwhile, the Commission urged EU nations to quickly seal deals with Nigeria and Tunisia to speed up the deportation process.
The EU says most African migrants are heading to Europe for economic reasons, making them ineligible for protection like that granted to asylum seekers fleeing war or persecution.
"We owe it to them, to our partners outside the EU, and to our citizens to be able to say clearly: when in need, we'll help, when not, you must return.
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