The Italian government on Saturday transferred hundreds of migrants to a ferry from a facility on the small island of Lampedusa.
The move aimed to relieve some of the severe overcrowding at the centre, although it remains hugely oversubscribed.
It follows a promise made by Prime Minister Giuseppe Conte during an emergency meeting with the Sicilian president, Sebastiano "Nello" Musumeci, on Wednesday night.
Musumeci had ordered the evacuation of all migrant camps in the region, which sparked a legal conflict with the central government.
An administrative court suspended Musumeci's decision, leading to the emergency meeting between the Sicilian leader and Conte.
After their transfer on Saturday, the migrants must spend 14 days in precautionary quarantine on board the vessel that picked them up, the GNV Rhapsody.
Lampedusa Mayor Salvatore Martello said 752 migrants were transferred on Saturday, none of whom had tested positive for the virus.
Due to an influx of migrants this summer — some of them rescued at sea, others reaching the island's shores without help — the Reception Centre of Lampedusa held more than 1,000 people despite having a capacity of less than 200.