By RANDAL C. ARCHIBOLD
LOS ANGELES — The federal government has pledged millions of dollars to make up for the environmental damage from building hundreds of miles of fences along the Mexican border through wilderness and protected lands.
In an announcement on Thursday, federal officials said the new spending was intended to resolve any conflict in the missions of the Departments of Homeland Security and Interior. The former is building nearly 670 miles of fences and other security equipment along the border, while the latter is charged with protecting and maintaining several hundred miles of public lands along the fence.
The officials said the Homeland Security Department would devote up to $50 million in the next year for “reasonable mitigation measures” to compensate for the damage or loss of animal and plant habitat and cultural areas like American Indian religious sites.
That compensation could include modifying the fence to curb flooding and to accommodate threatened and endangered species or restoring their habitats, but officials have not worked out those details and it will vary depending on the area.
The Interior Department will draft a list of priorities by June.
The agreement between the two departments has been in the works since April, when the homeland security secretary, Michael Chertoff, to the dismay of environmentalists and some scientists in the Interior Department, used his Congressionally authorized power to waive environmental laws to speed access to broad swaths of land.
At the time, in the face of an outcry from critics, Mr. Chertoff said the fence construction would proceed but with sensitivity to the environment and in coordination with the Interior Department.
Homeland security officials said the department had spent about $40 million in the past two years to address environmental problems associated with the border security project.
The fence construction and related roads and equipment for detecting illegal border crossers directly affect 200 to 300 miles of Interior Department land along the fence route and some of the most environmentally sensitive sites in the region.
With the promise of new spending coming just days before President-elect Barack Obama takes office on Tuesday, it was unclear on Friday to what extent the agreement would stick.
Gov. Janet Napolitano of Arizona, a Democrat whom Mr. Obama has chosen to head the Homeland Security Department, has not publicly taken a position on Mr. Chertoff’s use of the waivers, a spokeswoman said.
But Ms. Napolitano has expressed skepticism about the effectiveness of the fence. On Thursday, she told a Senate committee considering her nomination that she planned a broad and thorough review of the department’s policies.
Nick Shapiro, a spokesman for the Obama transition office, said, “President-elect Obama will review all 11th-hour regulations and will address them once he is president.”
Lloyd Easterling, a spokesman for Customs and Border Protection, the agency within the Homeland Security Department that will decide how to spend the $50 million, said transition officials were consulted on the agreement and took no position. But Mr. Easterling expressed optimism that it would go forward.
“Good environmental stewardship,” he said, “is transcendental of administrations.”
Environmental groups who challenged the fence construction, including an effort to have the Supreme Court block it, said dozens of species had suffered lost or damaged habitat. Among them, they say, are jaguars, ocelots, deer, javelinas and owls.
The environmental groups said that although steps to minimize the environmental harm of the fence were welcome, they would press the new administration to halt further fence building and reassess what had been done.“We heard in Janet Napolitano’s remarks this week interest in evaluating this project, and that certainly is what the Sierra Club is asking for,” said Oliver Bernstein, a spokesman for that group in Texas. “This $50 million is too little, too late, but it is recognition that the border wall project is having tremendous environmental consequences.”
A version of this article appeared in print on January 17, 2009, on page A15 of the New York edition.