The proposal involves admitting refugees to European Union countries over the next two years under the bloc's resettlement programme, 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.
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".
Resettlement would continue from those areas but there would be "increased focus" on North Africa and the Horn of Africa -- particularly Libya, Egypt, Niger, Sudan, Chad and Ethiopia, the commission said.
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"This will contribute to further stabilising migration flows along the Central Mediterranean route," which mainly involves people making the dangerous crossing from Libya to Italy, it said.
The resettlement programme is different from the EU's controversial refugee quotas, which involved moving asylum- seekers who had already reached Italy and Greece to other EU countries, under compulsory quotas.
Brussels separately released plans today to allow countries in the passport-free Schengen area to reintroduce border controls for security reasons for up to three years.
Countries in the 26-country Schengen travel area can currently reintroduce frontier checks for six months for security reasons, and two years if that is combined with a threat to borders such as Europe's migration crisis.
"Under today's proposals, member states will also be able to exceptionally prolong controls if the same threat persists," the European Commission, the executive arm of the EU, said in a statement.
Several countries including France and Germany have called for the extension after a series of terror attacks. France reinstated the checks after the November 2015 Paris attacks.