Charities that rescue migrants attempting the perilous Mediterranean crossing on Wednesday condemned Italy for its decision to close its ports because of the coronavirus epidemic.

The interior ministry said late on Tuesday that Italy could no longer be considered a "port of safety" for the duration of the outbreak, which has killed over 17,500 people in the country.

That means migrants rescued at sea cannot be disembarked in Italy.

The closure comes a month after Italy was put on a nationwide lockdown in a bid to stem the virus's spread.

Doctors Without Borders (MSF), Mediterranea Saving Humans, German maritime rescue group Sea-Watch and Spanish Open Arms accused Rome of using the crisis as an excuse to stop taking in migrants.

"At a time like this, the suffering of citizens affected by a health emergency cannot become a reason to deny support... to those who risk losing breath not in an intensive care bed, but by drowning.

"All lives must be saved, all vulnerable people must be protected, both on land and at sea. It is possible and necessary to do so," they said.

The four charities pointed out that they had all put resources and personnel at the disposal of the Italian health system for the coronavirus battle. And that providing safe harbour to those saved at sea was "a legal obligation".

The Alan Kurdi vessel, run by the German NGO Sea Eye, was seeking a safe port after rescuing some 150 people off Libya Monday, including a pregnant woman.

The interior ministry says nearly 3,000 migrants have landed in Italy so far this year.

Departures from Libya are expected to increase as the situation there deteriorates.

"A year into the conflict, the humanitarian situation in Libya has never been worse," the International Organisation for Migration's Libya mission chief Federico Soda said in a statement Wednesday.

Aid workers were finding it increasingly difficult to access the vulnerable, and security challenges were now coupled with grave health concerns posed by the potential spread of the COVID-19 virus, he said.

On Wednesday, Malta sent a diplomatic message to Germany, informing it that it would not allow migrants rescued at sea by NGO ships to disembark here.

In a conference call between EU foreign ministers last week, Foreign Minister Evarist Bartolo urged member states to take responsibility for sea rescue vessels flying their respective flags.