Duke Energy agreed on Friday to pay $1 million in fines as part of the Justice Department’s first criminal case against a wind power company for the deaths of protected birds.

A subsidiary of the company, Duke Energy Renewables, pleaded guilty in Federal District Court in Wyoming on Friday to violating the Migratory Bird Treaty Act, a federal law that protects migratory birds. The company was charged with killing 14 golden eagles and dozens of other birds at two wind projects in Wyoming since 2009.

In a plea agreement, the company said it would pay the fines to several conservation groups, including the North American Wetlands Conservation Fund, the Wyoming Game and Fish Department and the National Fish and Wildlife Foundation. The company must also put a plan in place to prevent bird deaths in the future, federal officials said.

“In this plea agreement, Duke Energy Renewables acknowledges that it constructed these wind projects in a manner it knew beforehand would likely result in avian deaths,” Robert G. Dreher, the acting assistant attorney general for the Justice Department’s environment and natural resources division, said in a statement.