The rescued migrants and refugees were traveling on three ships: the Aquarius, operated by the charities SOS Méditerranée and Médecins Sans Frontières (MSF), an Italian naval ship and an Italian coastguard vessel.
Aquarius, which was originally carrying more than 600 rescued migrants, was left stranded in the Mediterranean for two days after Matteo Salvini, Italy's hardline interior minister and leader of the anti-immigration League party, refused to allow it to dock last Sunday. After Spain offered to take in the survivors, the ship started an 800-mile journey to the city of Valencia
along with the two Italian ships, which were sent to ease the overcrowding.
Conditions on board the Aquarius worsened on Wednesday as poor weather and large waves caused dozens of people to suffer from seasickness.
At least 80 people who were pulled out of the sea by rescuers over the weekend had to be treated by doctors as waves as much as four meters high and winds of 65 kilometers per hour buffeted the vessel, according to Doctors Without Borders (MSF), which operates the rescue ship alongside SOS Méditerranée.
That included pregnant women and a mother "who was breastfeeding her baby while vomiting at the same time," Aloys Vimards, MSF project coordinator on board the Aquarius, told CNN.
"In the evening, we had to move the men sleeping on the outside deck to the shelter usually reserved (for) women and children, for safety reasons," SOS Méditerranée's Julie Mélichar told CNN.
Around 250 people were transferred from the Aquarius to the Italian Navy's Orione and a further 274 to the Coast Guard vessel Dattilo, SOS Méditerranée said.