More than 500 migrants Wednesday began disembarking a rescue ship for health checks in Sicily after nearly two weeks at sea, an NGO and the national news agency said.

Italy's interior ministry Tuesday allowed the Geo Barents carrying 558 migrants to dock in the port of Augusta, the ship's operator Doctors Without Borders (MSF) said on its Twitter page.

On Wednesday morning, health workers started administering the migrants Covid tests, while three people were transferred to hospital, Italian news agency AGI reported.

The ship departed on December 15 and made eight rescues, Doctors Without Borders said.

The migrants it has rescued include one woman who is eight months pregnant, unaccompanied minors, and "people who have endured sexual violence and horrific abuse", the non-governmental group wrote on Twitter. 

After administrative and health procedures, the migrants will undergo a quarantine, AGI said.

Still awaiting a port of entry is the Sea-Watch 3, operated by Germany's rescue charity Sea-Watch, with 440 migrants on board. Four people were evacuated from the ship on Tuesday. 

The UN refugee agency estimates that 114,584 migrants have arrived by sea this year to Italy, Greece, Spain, Cyprus, and Malta.

The number of sea arrivals is greater than last year, with 95,031 recorded, but still far short of the over 1 million people who arrived by sea in 2015. 

The group reports the number of dead and missing migrants this year as 1,839.

On Wednesday, during his weekly general audience at the Vatican, Pope Francis called the migration crisis "humanity's social scandal".