“We have been left in the lurch at sea, we can't go anywhere,” Captain Pascual Dura of the “Nuestra Madre Loreto” told AFP by telephone.
Since Thursday the 13 crew members of the fishing vessel have hosted 12 migrants from Niger, Somalia, Sudan, Senegal and Egypt who they rescued from a rubber dinghy that had set sail from Libya to Europe.
Italy and Malta have refused to allow the boat to dock and unload the migrants while Spain's maritime rescue service only offered to return the migrants to Libya, Dura said.
“If we go to Libya, we run the risk of a mutiny… when they hear the word Libya they get very nervous and hysterical, it is hard to calm them down,” he added.
“We don't want to return them to Libya. After they managed to get here, we don't want to return them to the place they are fleeing from.”
Abuse of migrants is widespread in Libya, following the chaos which has reigned since the 2011 ousting of dictator Moamer Kadhafi.
Many migrants, intercepted or rescued at sea, find themselves held in detention centres in the country in dire conditions.
Dura said the ship only had enough provisions and fuel for “six or seven” more days and a storm was approaching.
Spanish Foreign Minister Josep Borrell confirmed that Italy and Malta refused to allow the fishing vessel to dock but added the situation “is not an emergency”.
The fact that the Spanish fishing vessel was operating in Libyan waters “complicates the situation”.
The regional government of Valencia, where the fishing vessel is based, offered to accept the migrants.
In June the Valencia government also offered to accept 630 migrants from the Aquarius charity-run rescue ship after Italy and Malta refused to harbour the vessel.
Spain then allowed the Aquarius to dock and the migrants were distributed among several European Union nations.
More than 106,000 migrants have arrived in Europe by sea since the start of the year, according to the International Organization for Migration, and at least 2,119 others have died in the process.