The new operation - dubbed Frontex plus after Europe's border agency - will replace the "Mare Nostrum" naval deployment launched by Italy after two deadly shipwrecks in 2013, which Rome has threatened to wind up without more help.
EU Home Affairs Commissioner Cecilia Malmström announced the new initiative after meeting Italian Interior Minister Angelino Alfano, who said recently that "responsibility for the Mediterranean's borders must belong to Europe".
Calling on members states to support the project, Malmström said she hoped the new operation "will succeed Mare Nostrum by end of November," with two existing Frontex missions, dubbed Hermes and Aenaes, merged together and "upgraded".
Rome has issued a series of warnings to its European allies over the migrant crisis, which it says has seen more than 100,000 people arrive in the country after making the perilous journey by boat since the start of the year.
Over the weekend, the bodies of more than 300 people were discovered by the Italian navy after their boats capsized or sank. Some 4,000 migrants were rescued between Friday and Tuesday, the navy said.
European borders agency Frontex earlier this month said the number of migrants arriving in Italy in the first half of the year had already topped the record set in 2011 during the Arab Spring uprisings.
"Our objective is to start Frontex plus and slowly phase out Mare Nostrum," said Alfano, after meeting the commissioner in Brussels.