Survivors from one boat that went down in Malta's search and rescue area told officials about 20 people on board were missing, a coastguard statement said.
Three people had been reported missing earlier after another shipwreck in Italian waters about 30 kilometres (20 miles) from the island of Lampedusa.
A body was later recovered from a third boat that sank in Malta's waters.
All three boats were intercepted by Italian authorities Sunday night and Monday, when 1,200 people were rescued and brought to Lampedusa, the coastguard said.
"During last night and up until now, 35 boats have been rescued from the Tunisian route alone," it said, adding that around 20 more vessels remained at sea.
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