The Mediterranean rescue ship Aquarius arrived at Valletta harbour in Malta on Wednesday to allow 141 migrants off, ending a five day tug-of-war among European Union countries which saw the vessel banned from docking in several ports.
The ship, run by the Franco-German charity SOS Mediterranee and Doctors without Borders (MSF), was allowed in after France, Germany, Luxembourg, Portugal and Spain agreed to take in the migrants, rescued off the coast of Libya.
Aid groups said there were more than 70 children on board.
The EU countries will also take some of 114 migrants rescued by Maltese armed forces and brought to Malta earlier in the week.
The row was the latest tussle illustrating how politically fraught the issue of coping with seaborne migrants remains despite a deal on migration EU leaders agreed on at a summit in June.
Malta initially argued migrants on board the Aquarius should be taken to Libya, Tunisia or the Italian island Lampedusa, all closer to the rescue points.
As the ship docked, members of a right-wing group Moviment Patrijotti Maltin (Malta Patriotic Movement) unfurled a banner reading “Stop Human Trafficking”. Next to them, crew of another rescue vessel, the MV Lifeline, held up a banner reading “Everyone has a right to life.”
A government spokesman said the migrants, mostly from Eritrea and Somalia, would be given an initial medical check before being taken to a reception centre.
This was the second time in as many months Aquarius was at the centre of a Mediterranean standoff. It was refused entry by Italy and Malta in June and the boat then docked in Spain, which took the migrants.