Coastal and inland surveys for the endemic and “Critically Endangered” Madagascar Fish Eagle Haliaeetus vociferoides were conducted in western Madagascar from Antsiranana in the north to Manja in the south during the 2005 and 2006 breeding seasons (May–October). Surveys covered typical Madagascar Fish Eagle habitat: lakes, rivers, mangroves, estuaries, and marine islands within their known distribution. In total, 287 individuals were encountered, including 98 breeding pairs (196 individuals), 23 breeding trios (69 individuals), 15 single adults and seven immature birds. Of these 287 birds, 128 individuals (44.6%) were observed on lakes; 116 (40.4%) in coastal areas, consisting of 103 (35.9%) in mangroves and 13 (4.5%) in estuaries; 32 (11.2%) on marine islands and 11 (3.8%) on rivers. There was an increase between surveys in 1995 and this study in the number of Madagascar Fish Eagles counted, from 222 to 287, and in the number of pairs from 99 to 121. This study confirms that the Madagascar Fish Eagle population is still low due to human persecution (hunting, collection of eggs and nestlings), overfishing and habitat destruction. We recommend monitoring fish eagles annually at the higher concentration sites to evaluate human activities and conducting a population survey every five years throughout western and northern Madagascar.