A Maltese patrol boat rescued about 80 migrants in a drifting dinghy off the island early on Thursday, but another 20 people were feared to have perished.
Along with southern Italy, Malta is one of the main points of arrival for migrants attempting the crossing from North Africa into Europe.
A government spokesman in the Maltese capital Valletta said the migrants appeared to have been in the dinghy for a number of days and needed medical treatment. He said they had told their rescuers that there had been 100 people in the boat, but 20 had died.
The nationality of the migrants is not yet known.
Malta has been pressing the European Union and Mediterranean rim states to cooperate in efforts to stem migrant arrivals and help send them back home, or integrate into European countries.
People smugglers have taken advantage of lawless conditions in Libya to send out hundreds of small, unseaworthy boats. Thousands have died during the crossings in recent years.
An Italian coastguard vessel picked up a separate boat carrying around 70 migrants off the coast of Libya on Thursday.
Arrivals from North Africa have slowed in recent months with more coming on larger cargo ships from Syria.
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