The migrant rescue ship MV Lifeline was allowed into Maltese territorial waters on Wednesday morning as heavy seas made conditions on board difficult.
The ship reported shortly after 10am that it had been granted permission to sail into Maltese waters.
It sought such permission at 11pm on Tuesday when its captain said a "huge number" of people on board were suffering sea sickness.
The ship has been idle off the Maltese coast for five days amid controversy after it picked up 234 migrants in the Libyan rescue zone in what Italy and Malta said was defiance of orders for the migrants to be rescued by the Libyan coastguard.
There are 70 unaccompanied minors on board, 14 women, three babies and a child.
Vor 1 Tag kamen die Eilmeldungen, dass wir auf Malta einlaufen dürfen, aber wir haben noch immer keine Genehmigung.— MISSION LIFELINE (@SEENOTRETTUNG) June 27, 2018
Wir fragen nun, ob wir uns wenigstens vor den hohen Wellen & dem starken Wind vor der maltesischen Küste schützen dürfen. Sehr viele sind seekrank. #lifeline #malta pic.twitter.com/yzHI5xhdqz
Malta indicated on Tuesday that it was ready to take the migrants on the understanding that they would be shared by several other EU countries.
By Wednesday morning five EU states - Italy, France, Portugal, Ireland and Malta - confirmed they are willing to take some of the rescued migrants.
Three other EU countries - Germany, the Netherlands and Spain - are also "evaluating" the case but there has been no reply. No other EU state is believed to have offered to help.
Lifeline points fingers at German minister
In a statement, early on Wednesday, the NGO pointed fingers at German Interior Minister Horst Seehofer for "blocking any solutions" since, insisting he was fighting the inner power play of his party on the back of people's lives and safety.
Axel Steier, co-founder of Mission Lifeline, said: "if the situation on the ship will escalate in the next hours due to exhaustion and weakness of the people rescued and the overall worsening weather conditions, it is entirely the responsibility of Mr Seehofer to bear the consequences. He acts like a German version of his Italian (right-wing) colleague Mr Salvini and makes the German government complicit to non-assistance to persons in danger.”
The Lifeline also gave its version as to why it defied orders to hand over the rescued migrants to the Libyan coastguard.
Doing so would have not been in line with the Geneva Refugee Convention and therefore criminal. The ship received the reply to disembark in Tripoli, which would have been a breach of the principle of non-refoulement, which is the practice of not forcing asylum seekers to return to a country in which they are liable to be subjected to persecution.
Lifeline said it would obey all instructions received from different maritime authorities as long as it was in compliance with international law.
The Maltese government has threatened legal action against the ship captain should he land in Malta.
NGOS concerned by talk of legal action
Meanwhile, Maltese human rights organisation Aditus has sprung to the Lifeline's defence, saying it was prepared to offer free legal services to the crew should action be taken against them.
"It was the the duty to rescue all persons in distress and to ensure their disembarkation at a safe port, in accordance with international law. We will stand by our NGO colleagues as they face bullying tactics from governments that have repeatedly ignored their legal and moral obligations," Neil Falzon said.
In a joint statement issued on Wednesday morning, a group of NGOs in Malta and Italy urged the EU and its member states to prioritise work to bring the stranded migrants ashore.
"Whilst we appreciate the need to clarify legal responsibilities, we emphasise that the protection of life and human dignity should remain the topmost priority," they said.
They also defended Lifeline's decision to defy orders to hand migrants over to Libya's coastguard, saying that allowing disembarkation in unsafe places "such as Libya" would violate international law and was therefore "not a viable option".
"Thus, we express our concern with the announcement made by both the Italian and Maltese authorities on the intention of sanctioning the captain and crew of the Mission Lifeline rescue ship."
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