McALLEN, Texas — The Department of Homeland Security will allocate as much as $50 million to mitigate the environmental impact of the U.S.-Mexico border fence ordered by the Bush administration.

The agency signed an agreement Wednesday with the Department of the Interior to set aside funds for projects that the Interior department determines will soften the environmental damage caused by the fence.

“Today’s signing of this memorandum of agreement demonstrates that our commitment is not only words, but actual resources, which have been set aside to allow DOI to mitigate the impact of our border security efforts in environmentally sensitive areas,” Customs and Border Protection Commissioner W. Ralph Basham said in a statement released Thursday.

The Department of Homeland Security includes Customs and Border Protection, which is overseeing the fence project.

The Department of Interior must give DHS its list of proposals by June 1.

The environmental consequences have been part of the loudest opposition to building 670 miles of pedestrian fence and vehicle barriers along the U.S.-Mexico border.

“It’s about time,” said Julie Hillrichs, spokeswoman for the Texas Border Coalition, a group of politicians and business leaders opposed to the fence. “DHS officials finally got around to doing what the Texas Border Coalition has been asking them to do for at least six months. We support it completely.”

Matt Clark, southwest representative for Defenders of Wildlife, said he expected the projects to target threatened and endangered species most affected by the fence.

“It demonstrates goodwill on the part of both agencies,” Clark said.

“We see this as a down payment; $50 million will not come close to fixing the damage caused by the wall. Some of these impacts may not be able to be offset.”

On April 1, Homeland Security Secretary Michael Chertoff used authority granted by Congress to waive a host of environmental protection laws sparking howls of opposition and lawsuits.

At that time, Chertoff promised the agency would be a good environmental steward even while the change allowed speedier construction of the fence.

In place of the established environmental impact statements that require a long list of extensive studies, the agency developed its own plans.

Some, including one for the Rio Grande Valley that would clear about 508 acres of land, acknowledged the fence would affect wildlife and “potential for gene flow” because some species cross the border into Mexico to mate.

Seventeen of the 21 fence sections in the Valley will affect wildlife management areas or national wildlife refuges, 14 of them directly.