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The Sea-Watch 4 vessel of the German NGO has been waiting for several days for port permission to disembark the rescued migrants in the central Mediterranean.
"The fierce struggle will continue throughout the night to bring the population to safety and protect homes," the fire service said on Twitter.
As they return to the seas for the first time since April, rescue ship operators say migrants fleeing Libya's humanitarian crisis are undeterred by Europe's coronavirus outbreak
News of the missing boat comes amid criticism of the European Union's lack of rescue missions in the Mediterranean Sea.
A Sudanese man was killed by a bullet would, the International Organization of Migration said.
The migrants were picked up in two separate operations off the coast of Libya, MSF, who runs the ship alongside SOS Mediterranee, said on Twitter.
I was invited to cruise on a superyacht in Malta, bringing me that little bit closer to what it would feel like to own one myself.
Experts say that warming oceans and rising sea levels will likely make hurricanes more intense and their impact more devastating.
France has become the first EU member state to say it would welcome some of the 356 migrants on board the stranded rescue ship Ocean Viking.