The proposal involves admitting refugees to European Union countries over the next two years under the bloc's resettlement progress, which was introduced during the migration crisis that hit the continent in 2015.
"We need to open real alternatives to taking perilous irregular journeys," European Union Migration Commissioner Dimitris Avramopoulos told a news conference in Brussels, AFP reported.
The European Commission said in a statement that it was "recommending a new EU resettlement scheme to bring at least 50,000 of the most vulnerable persons in need of international protection to Europe over the next two years".
The EU has already resettled 23,000 people from refugee camps in countries outside the EU under the scheme, particularly Turkey and Jordan, which were overwhelmed with people fleeing the war in Syria.
Resettlement would continue from those areas but there would be "increased focus" on Libya, Egypt, Niger, Sudan, Chad and Ethiopia, the commission said.
"This will contribute to further stabilizing migration flows along the Central Mediterranean route," which mainly involves people making the dangerous crossing from Libya to Italy, it said.
The resettlement program is different from the EU's controversial refugee quotas, which involved moving migrants who had already reached Italy and Greece to other EU countries under compulsory quotas, and which ended on Wednesday.