The huge energy supplier agreed to the sum after pleading guilty to charges over the deaths of 14 eagles in the past three years at the Wyoming site.
It is the first time the Obama administration has taken action against a wind energy company in such a case, the AP news agency report.
The fines will go to wildlife and wetlands conservation bodies.
The charges were brought under the Migratory Bird Treaty Act, which protects golden eagles as well as other species.
According to one study by federal biologists in 2013, wind energy facilities in 10 US states have killed at least 67 golden and bald eagles since 2008, AP said.
The eagles often fail to look up as they search for prey until it is too late, slamming into the turbines. They can also be sucked in by the tornado-like vortex created by the fast-moving blades.
Duke Energy Renewables president Greg Wolf said the company “deeply regretted” the impact to golden eagles at two of its wind facilities, and had been working closely with the US Fish and Wildlife Service to “take proactive steps to correct the problem”.
These have included installing radar technology to help detect eagles in flight nearby and further curbing turbines at times of high eagle flight activity.
Duke Energy Renewables is the renewable energy arm of Duke Energy. This corporation, with market capitalization put at around $50 billion, says it is the largest electric power holding company in the US, serving more than seven million customers.
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