Italian media report that the women's bodies are being kept in a refrigerated section of the warship. Most of them were aged 14-18.
Five of the surviving migrants have been questioned about what happened to the women, some as young as 14, and they identified two men who are believed to have captained one of the boats.
Most of the 375 survivors brought to Salerno were sub-Saharan Africans, from Nigeria, Senegal, Ghana, The Gambia and Sudan, the daily La Repubblica reports.
Among them were 90 women - eight pregnant - and 52 children.
Migrants disembark from the Spanish ship 'Cantabria' in the harbour of Salerno, Italy. Photo / Getty Images
Some believe the girls were victims of sex trafficking, but experts believe otherwise.
"Sex trafficking routes are different, with different dynamics used. Loading women on to a boat is too risky for the traffickers, as they could risk losing all of their 'goods' - as they like to call them - in one fell swoop," Salerno prefect Salvatore Malfi told the Italian press.
One of the survivors, Dora Omoruyi, a 23-year old arts student from Benin, Edo State, said she left Nigeria because of the lack of employment opportunities.
Rescued migrants disembark from the Spanish navy ship 'Cantabria' on November 5, 2017 in Salerno, Italy. Photo / Getty Images
She said: "I wanted to reach Italy. I don't know what to do now.
