Cyclone Ernest struck Faux Cap, the southernmost tip of the huge Indian Ocean island, on Sunday generating winds of up to 100 kph (60 mph). One child drowned in the coastal town of Tulear, and up to 1,340 people across the country were left homeless as flood waters swelled, washing away their houses, officials said.
Some 103 people were injured, many by falling trees and collapsing roofs.
Emergency recovery teams are still looking for the fishermen, who were out at sea when the storm struck.
"We are searching for them. Nothing has yet been found," emergency council secretary general Jacki Randindrarison told Reuters.
Catholic Relief Services country director Jennifer Overton said 600 hectares (1,480 acres) of paddy fields had been flooded.
"We're worried that this will cause food shortages later in the year," she told Reuters, adding that the aid agency was ready to distribute 400 metric tonnes of food.
"We're hoping to respond with WFP (World Food Programme). We already have food in the region and staff on the ground," Overton said.
About five or six tropical cyclones hit Madagascar every year. The island suffered its worst damage in decades last year when cyclones Elita and Gafilo struck in January and March, killing 295 people, ravaging crops and leaving 300,000 homeless.