The storm had headed back to sea on Sunday and had been stationary off the western city of Morondava for more than two days, the office said.
The storm and rain had so far displaced just over 60,000 people and damaged 13,000 houses and 100 classrooms, the European Commission's Civil Protection and Humanitarian Aid Operations department said in a statement on Thursday.
Madagascar and Mozambique in recent years have been repeatedly hit by severe storms and cyclones that have destroyed homes, infrastructure and crops and displaced large numbers of people.