Instead, the deal sees the migrants transferred soon on Maltese military vessels to bring them ashore, while the private boats won't be allowed to dock.
Malta now cleared the way for them to disembark.
Germany expects to take in 60 migrants who were already in Malta or are about to arrive there under an agreement to defuse the latest standoff over rescue ships in the Mediterranean Sea.
The eight countries that will take them in include Italy, whose anti-migrant interior minister, Matteo Salvini, had vowed for days that none would reach Italian soil.
The deal, announced by Maltese Prime Minister Joseph Muscat, breaks a stalemate that began after 32 were rescued by a German aid group's vessel on December 22.
The German humanitarian vessel Sea-Watch 3 rescued 32 people near Libya on 22 December and its sister ship, Sea-Eye, collected 17 more on 29 December.
According to the Telegraph, of the total, 176 would be sent to Germany, France, Portugal, Ireland, Romania, Luxembourg, the Netherlands and Italy.
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.
EU Migration Commissioner Dimitris Avramopoulos said Wednesday that "the past weeks have not been Europe's finest hour".
"This represents a confession of state failure, policy must not be made at the expense of people in distress", the NGO said. European Union border agency Frontex says about 57,000 migrant crossings were detected past year in Spain, twice as many as during 2017.
Amnesty International's Southern Europe researcher Elisa De Pieri said the time taken to reach a decision on the migrants' fate was "shameful".
"Malta is a very small country", he said.
The call has been shared by Italy's protestant community, with evangelicals offering to take in some of the migrants.
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.
Seventeen people on board another ship and 249 rescued migrants already in Malta will also be divided up between the eight countries as part of the deal, Malta said.
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