The Alan Kurdi has been stuck at sea with 80 people on board for nine days.
Another woman was evacuated from a stranded humanitarian vessel after requiring medical attention, the government said.
NGO Sea-Eye said in a statement the woman, 23-year-old Nigerian, one of the two pregnant women on board the Alan Kurdi, had suffered an epileptic seizure. Her "worried" husband remains on board.
The vessel has been stuck at sea for nine days with 80 people aboard - 64 of whom were rescued off war-torn Libya. On Tuesday, another 24-year-old woman was evacuated to Malta for medical attention by the AFM following loss of consciousness.
The ship has been denied access to Malta and Italy, with both governments repeatedly saying it was Libya's responsibility to take in the boat, Sea-Eye chairman Gorden Isler had told Times of Malta.
"We can only hope that the young woman will soon feel better again. Here on board we could not help her anymore," Capt. Werner Czerwinski said.
He expressed his concern about the coming days saying the people were constantly asking him why they had to stay on board for so long.
“They are really afraid of the next phase of bad weather. Many of them were seasick and recover only slowly. They see how two women collapsed and had to be evacuated. This is not a condition for people who have experienced such terrible things and it is also not a condition for my crew," he said.
The Migrant Offshore Aid Station delivered emergency food, water, medicines, dry clothing and blankets to the remaining migrants onboard the stranded vessel Tuesday afternoon. Another shipment had to be delivered by the AFM.
The woman’s evacuation was one of two medical evacuations carried out by the AFM on Wednesday.
In a statement, Sea-Eye, said it was still waiting for a political solution.