The crew of the Maersk Etienne picked up the migrants fleeing from Libya on August 4th following a request from Malta.
But Maltese Prime Minister Robert Abela has since said his country is not responsible for them.
The three organisations — the UN Refugee Agency (UNHCR), International Organization for Migration (IOM) and International Chamber of Shipping (ICS) — accused governments of breaking international law by refusing to allow the migrants to leave the ship.
The organisations did not single out Malta, instead calling for coastal EU countries to step up and for other EU nations to show solidarity by accepting relocated migrants.
“The conditions are rapidly deteriorating on board, and we can no longer sit by while governments ignore the plight of these people,” said ICS Secretary-General Guy Platten.
“Time is running out and the responsibility for these people's safety and security rests squarely with government ministers.”
Danish shipping giant Maersk revealed on Sunday that three of the migrants jumped overboard before crew members rescued them.
They said commercial vessels were not equipped to rescue or house migrants.
According to the Danish press, the migrants' boat had drifted in Tunisian territorial waters.
Denmark believes that “Tunisia is responsible for welcoming these people,” Danish interim foreign minister Kaare Dybvad Bek told AFP.
“The government is ready to help the Tunisian government,” he added in a written statement.
UNHCR chief Filippo Grandi called on the EU and its member states to “show some solidarity” and set up “an effective relocation mechanism.”
“The absence of a clear, safe, and predictable disembarkation mechanism for people rescued in the Mediterranean, continues to pose an avoidable risk to life,” added IOM Director General Antonio Vitorino.
According to the joint statement, the Etienne is the third commercial vessel to rescue migrants so far this year, but the other ships found places to disembark the migrants in just a few days.
In the first half of the year, 14,481 people took to the sea from Libya trying to reach Europe, according to UNHCR figures.
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