Prime Minister Joseph Muscat tweeted that while the rescues didn't happen in the Maltese search-and-rescue area, Malta was letting SeaWatch 3 and another vessel enter Maltese waters. The German aid group operating SeaWatch 3 says 32 migrants were rescued from a human trafficker's boat on Dec. 22 and another vessel later rescued 17 others.
Sea-Watch Italy tweeted on Thursday it was a few nautical miles from Malta's coasts and had "permission to seek shelter from the storm." It said European Union officials were trying to find countries which would accept the migrants.
Malta and Italy have refused to accept migrants rescued by private groups.
British officials say two men have been arrested on suspicion of smuggling migrants from France to England by sea.
The National Crime Agency said late Wednesday that a 33-year-old Iranian citizen and a 24-year-old British man were arrested in Manchester.
The men are being questioned but have not been charged or identified. They are suspected of smuggling migrants across the English Channel in small boats.
The arrests are the first since Britain's Home Secretary Sajid Javid declared a rise in migrant crossings to be a "major incident." He is considering asking the Royal Navy to help patrol the Channel.
Javid says about 230 migrants tried to cross the English Channel in December. Officials have blamed the influx on smuggling gangs.