Loud cheers could be heard from the ship as it pulled into the Grand Harbour in Valletta, five days after the migrants, most of them Somalis and Eritreans, were rescued off Libya. Some flashed peace signs and waved from the deck.
Malta and Italy both initially refused to let the Aquarius dock in a re-run of the standoff seen in June when the vessel was at the centre of a heated diplomatic crisis between European governments.
But Malta on Tuesday agreed to reverse its decision as France, Germany, Luxembourg, Portugal and Spain offered to take in the ship's latest passengers, along with 114 others who arrived on the island on Monday.
The Maltese government said later that Italy had agreed to take some of the migrants but did not say how many.
The Aquarius was allowed to dock despite Malta having “no legal obligation to (allow it to) do so,” the government said in a statement later.
The migrants were unloaded from the Aquarius straight onto police buses to be taken to a reception centre, officials said.
Dozens of children were on the ship — more than 30 of them unaccompanied, according to a Maltese government source — while two heavily pregnant women were taken to an ambulance.
The Maltese authorities said separately that a military patrol vessel had rescued about 35 migrants on a small boat southwest of the island.
The Aquarius, chartered by French charity SOS Mediterranee as well as Doctors Without Borders, suffered a setback this week when Gibraltar said it would not longer be able to operate under the British territory's maritime flag.
But SOS Mediterranee's German wing said Wednesday that it would likely continue operating under a German flag if the dispute is not resolved.
“The Aquarius of course has the intention and obligation to set sail again as soon as possible, back into the rescue zone off the Libyan coast,” said the group's Germany chief Verena Papke.