If granted, the permit would be the first of its kind since legislation introduced in 1940 banned anyone from killing or disturbing the birds, their nests or their eggs without such a permit.
Under regulations adopted in 2009, the conservation agency can authorise the "take" of eagles for activities that are otherwise lawful but can result in disturbance or death.
West Butte Wind Power has applied for the permit for its 104MW project in Oregon. No eagle roosts have been found in the project area but the company has committed to implement mitigation measures regardless of eagle deaths.
It has also pledged extra measures in response to each dead eagle if the wind farm is found to be the cause. These include changing the cut-in speed from 3 metres per second to 5m/s at certain times of the year when eagles are more active and a $20,000 payment for conservation work for eagles.
The draft environmental assessment is open to comment till 2 February.