The Maltese Prime Minister, Joseph Muscat, according to information published here, specified that the people will be picked up by a military ship, from where they will be transshipped and redistributed to the eight European Union nations mentioned.
Malta had refused to allow the rescue ships to dock, saying it was not the nearest port of call and that taking responsibility for the migrants was beyond the remit of the EU's smallest member state.
A mother and a child disembark from a patrol boat in Malta.
Malta's Prime Minister Joseph Muscat addresses a press conference at his office in Valletta, Malta January 9, 2019.
The 49 migrants, rescued on December 22 and 29, were aboard the Sea Watch 3 and Albrecht Penck NGO vessels.
The deal also involves the resettlement of more than 100 other migrants already in Malta, he announced.
Now, after coming closer to the Maltese coasts, according to internal sources of the Community bloc, the migrants will be sent to Germany, France, Portugal, Ireland, Romania, Luxembourg, the Netherlands and Italy, or repatriated. "Every hour that passed without a solution was not an hour I was proud of", he said.
He said an agreement had also been reached for 249 other migrants brought to Malta by its military patrol boats in December to be redistributed around the European Union or sent back to their country of origin.
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"After 19 days at sea, our guests finally have a safe haven", Sea-Watch tweeted.
"This represents a confession of state failure, policy must not be made at the expense of people in distress", the NGO said.
Minister for Justice Charlie Flanagan said five unaccompanied child migrants would be taken in from Malta as a gesture of solidarity and humanitarian assistance.
"We welcome this show of solidarity and understanding that Malta is going beyond what is required of us", said Mr Muscat.
The migrants at the center of the EU-brokered deal are among the waves of people from Africa, Asia and the Middle East who fled poverty and armed conflicts and risked their lives aboard smugglers' boats bound for Europe in recent years.
The exact number of migrants that Italy has agreed to host has not been announced, but Conte had previously indicated that Rome was willing to welcome around 15.
The European Union's border agency Frontex says about 57,000 migrant crossings were detected past year in Spain, double the figure for 2017.