A boat belonging to a Spanish aid group rescued 311 migrants off the coast of Libya including a mother and child on Friday.
The vessel will take the migrants to Algeciras in Spain after Malta reportedly denied the boat permission to dock at its ports, Reuters said.
Open Arms has not received official permission to dock but have been told by port authorities in Spain to head there.
The charity, Proactiva Open Arms, operates between Libya and southern Europe.
A newborn baby and his mother were, however, evacuated by helicopter to a hospital in Malta, the charity's founder Oscar Camps said in a tweet on Saturday.
Italy also denied the vessel entry and Deputy Prime Minister and Minister of Interior Matteo Salvini tweeted on Saturday that "Italian ports are closed! For the traffickers of human beings and for those who help them, the godsend is over."
Euronews contacted Malta's Foreign Affairs and the Spanish Ministry of Foreign Affairs.