The 224 migrants include some which were among a group of 249 rescued by the AFM over the Christmas period.
The deal calls for 300 migrants to be redistributed between eight countries, including Ireland.
PM Joseph Muscat named them as Germany, France, Portugal, Ireland, Romania, Luxembourg, the Netherlands and Italy.
In a tweet, Sea Watch International said: "The EU made a decision to release their 49 hostages".
EU Migration Commissioner Dimitris Avramopoulos said Wednesday that "the past weeks have not been Europe's finest hour".
Thanking civil society for its support, Sea Watch commented: "Disembarkation can not be subject to negotiations between states at the expense of people".
39;Sea-Eye' docked in Malta in December
European Union rules oblige countries where migrants first land to process any asylum claims, placing a heavy burden on Mediterranean states like Italy, Greece, Spain and Malta.
Alter said eight countries have now indicated their willingness to take in the migrants but talks are ongoing with more.
But with no country allowing them to dock, they were left stranded off the coast of Malta, suffering sea sickness and dehydration, with some briefly refusing food and an onboard doctor warning of psychological stress.
"We were not the responsible authority, and we were not the nearest safe port" for the two rescue vessels, Mr Muscat said.
The migrants involved in the EU-brokered deals are part of waves of people fleeing poverty and conflict in Africa, Asia or the Middle East, who have risked their lives aboard smugglers' boats to try to reach European shores in recent years.
The deal means the 49 migrants, who have been stranded on charity-run boats amid a row over who would take them, can now disembark in Malta.
"I am and I will remain absolutely against new [migrant] arrivals in Italy", he said on Twitter.More news: Iran's foreign ministry confirms arrest of former USA sailor
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