The rescue took place off the Libyan coast late Wednesday and the migrants will be brought to Malta, the Maltese military said in a statement.
It said it had coordinated multiple joint rescue operations in conjunction with the Italian coastguard and "in support of the Libyan coastguard".
Malta has appealed to the EU for help in dealing with the flow of migrants, which its much larger neighbour Italy has begun to turn away.
The island of 450,000 people is a common destination for migrants trying to cross the Mediterranean from North Africa, and a hardline stance from Italy has increased pressure on it.
More than 500 migrants have reached Malta this year, while 1,425 have made it to Italy, which has a population 130 times larger.
International Organization for Migration figures show 24,687 migrants have reached Europe so far this year, well below the record of around one million in 2015, and 144,000 last year.
Among EU member states, Spain took in the most migrants last year, at around 65,000.
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