The three survivors were transferred to a patrol boat and landed in Malta on Thursday afternoon.
The military said the missing were 21 men and four women.
There was no immediate word on where they had come from.
Officials said migrant flows across the Mediterranean had increased since patrols by Frontex, the EU's border control agency, ended early this month.
Another boatload of 30 migrants arrived in Malta on Thursday.
Two more two boats arrived the day before.