Lawyers for Defenders of Wildlife and the Sierra Club filed a complaint in U.S. District Court challenging the 2005 Real ID Act, which granted Secretary Michael Chertoff that power. The groups contend the law violates the constitutional separation of powers.
Chertoff invoked the power this month to override a federal judge's ruling delaying construction of a two-mile section of fence in the San Pedro Riparian National Conservation Area near Naco, Ariz.
Chertoff waived 19 environmental, conservation and cultural laws to restart the construction and build seven more miles of fence.
He earlier used that authority to finish construction of a fence in San Diego and one different one in Arizona.
"The secretary's action was a clear and unprecedented abuse of authority and demonstrated a profound disregard for the system of checks and balances assured in our Constitution. The secretary left us no choice but to address the unconstitutional nature of the Real ID act," Rodger Schlickeisen, Defenders of Wildlife president, said in a statement.
The department had no immediate comment.
Chertoff has said his agency extensively examined environmental issues for the Arizona fence and acted to mitigate the effects on the environment. He has argued that illegal immigrant traffic through the area already is damaging the environment.
Robert Dreher, vice president for conservation law for Defenders of Wildlife, said Congress deferred its lawmaking responsibility to Chertoff by giving him that authority.
Carl Pope, the Sierra Club's executive director, said in a statement that "arbitrarily waiving environmental protections is an extreme path to tread."