Spanish charity Proactiva Open Arms say the Asso 28, an oil rig support vessel rescued them from international waters on Monday and took them to Libya, their country of departure.
Migrants rescued in international waters cannot be returned to a place where their lives are put in danger.
Both the UN and European Union have acknowledged that Libya is not safe.
Italy’s coast guard initially said on Tuesday that the rescue was coordinated by the Libyan coast guard, and later clarified that the operation had taken place in Libya’s so-called “search and rescue (SAR)” area.
The Libyan coast guard was not immediately available for a comment.
Libya’s SAR is not clearly defined but is widely understood to extend far beyond its national waters.
A spokesman for the U.N. migration agency said the agency was still investigating the case but confirmed the return of the migrants to Libya.
He said the Libyans first told him the rescue operation was carried out by “an unknown vessel”, then changed their version and said the rescuing boat was Libyan.
The head of mission at Open Arms, Fabrizio Gatti, contradicted the Libyan version and said a member of the Asso 28 crew told him over the phone the Italian boat carried out the rescue and was taking the migrants back to Libya. He said he had a record of the conversation.
Asso 28 is now docked in Tripoli, the Libyan capital, according to Marine Traffic, a real-time information service on ships movements.
The rescue coincides with a growing perception among human rights groups that some European countries are taking an increasingly hard line in their efforts to cut the number of migrants arriving on their shores, after Italy’s new government closed its ports to charities’ rescue boats in past weeks.
Read on EuroNews