Understanding the interaction between eagles and wind farms is essential for the development of strategies to minimize collision risk, and to quantify avoidance rates for collision risk modeling. The purpose of our study was to measure the avoidance rates of Tasmanian wedge-tailed eagles (Aquila audax fleayi) and white-bellied sea-eagles (Haliaeetus leucogaster) using a new method, and to examine factors affecting these rates. We conducted eagle surveys at the Musselroe Wind Farm (undeveloped and used as a control); Studland Bay Wind Farm during commissioning and operational stages; and Bluff Point Wind Farm during the operational stage, all in northern Tasmania, Australia. Observers documented flight tracks and behavior of eagles over 875 days during the period 2006–2008. Both species demonstrated a distinct avoidance of the turbines, preferring to fly midway between them. Avoidance rates were 81%–97%, and differed significantly between species and sites, with white-bellied sea-eagles avoiding at a higher rate than wedge-tailed eagles. Eagles at Bluff Point had a higher avoidance rate than those at Studland Bay, even though the sites were only 3 km apart. Both species altered their avoidance rates in response to stages in the wind-farm development, but only the wedge-tailed eagle altered its rate in response to weather conditions, demonstrating a higher avoidance rate during wet and windy conditions. Our study found that the interaction of eagles and wind turbines is complex, which highlights the need for further study of avoidance rates in species at different sites.