Republican lawmakers are calling on the Interior Department to stop charging what they describe as "extortion" money from the Border Patrol -- millions of under-the-radar dollars meant to cover environmental damage stemming from their everyday duties along the U.S.-Mexico border.

The Department of Homeland Security, which houses the Border Patrol, last year signed a deal with Interior -- the administrator of America's parklands -- to cough up $50 million for environmental "mitigation" needed in the wake of the construction of a border fence. That was after DHS had already spent or committed millions more for expected environmental damage caused by the Border Patrol over the years.

Though both the departments of Homeland Security and Interior say the money goes toward preserving and restoring sensitive habitats, Republicans say the arrangement doesn't make sense.

The Border Patrol needs that money to address the weighty task of securing the border, they say, arguing that agents are actually helping conserve the environment by keeping out smugglers and immigration violators who have no regard for America's natural resources.

They note that the transactions are conducted with little congressional oversight, and the Border Patrol has privately described the routine negotiations as a "constant headache."

"It was a pay-to-play type of scheme," a Republican aide on the House Natural Resources Committee said of the millions Homeland Security has spent to date.

Rep. Rob Bishop, R-Utah, said the kicker in the multimillion-dollar tradeoff is that the money doesn't even guarantee the Border Patrol open access to the land. Agents still have to follow particular rules to drive into wilderness areas to pursue suspects or set up routine patrols.

"That conflict has got to be resolved," he said. "If the Border Patrol was allowed to have free access to patrol the borders at will ... it would have the same effect that they're doing in other areas."

Bishop in March called on Interior Secretary Ken Salazar to stop "extorting" the money from Homeland Security. "Money appropriated for border security should only be spent on making our borders more secure, and not diverted to unrelated DOI spending projects," he said in a statement at the time. According to Bishop's office, Salazar has not responded.

Interior Department spokeswoman Kendra Barkoff said in a statement to FoxNews.com that Salazar is trying to "meet the twin goals of protecting our national security and our natural resources" and has directed senior staff to work with Homeland Security to improve collaboration. She said "significant progress" has been made.

Environmentalists say the harm to the environment from border security efforts, particularly the massive border fence, is great. Defenders of Wildlife, an organization that has focused on the issue, argues that fence construction along the U.S.-Mexico border is cutting off animal migration routes, disturbing natural habitats and worsening flooding.

Defenders of Wildlife and the Sierra Club fought the Bush administration several years ago over its decision to waive certain environmental restrictions to ease construction of the border fence.

According to a letter by Salazar to Bishop sent in December, aside from the $50 million agreement, since 2006, $811,000 in "mitigation funds" had been transferred from Homeland Security to Interior for conservation of the Sonoran pronghorn, an animal similar to an antelope.

That conflicts with a letter sent two months earlier from Homeland Security Secretary Janet Napolitano to Bishop in which she claimed DHS had spent or committed $9.8 million between September 2007 and October 2009 -- money sent to both the Interior Department and Forest Service, which falls under the Department of Agriculture. That's in addition to millions more that Homeland Security said it spent itself on "surveys and mitigation efforts" for the benefit of threatened and endangered species.

Plus the Border Patrol has set aside $5 million to "offset" negative effects to the environment from the construction of sensor towers along the Arizona border, according to DHS estimates. Those towers are part of a broader border security initiative that was partially halted earlier this year pending further review.

According to an impact study released in December, mitigation money for the towers along a 30-mile stretch of U.S. border was to be spent on a dizzying series of environmental projects. They include:

-- $200,000 to study the extent of unauthorized vehicle routes in the habitat of Sonoran pronghorn, which are endangered.

-- $1.75 million to close and restore those vehicle routes.

-- $20,000 to move pronghorn back to the Valley of the Ajo if they don't migrate by themselves in three years.

-- $14,000 to do weekly aerial surveys of the pronghorn during the 2010 fawning season.

-- $35,000 for monitoring the maternity roosts of lesser long-nosed bats.

-- $140,000 to study "unknown roosts" for lesser long-nosed bats.

Matt Clark, southwest representative for Defenders of Wildlife, described those examples as "well-thought-out mitigation measures." He said the towers might not look harmful to the environment, but that the generators attached to them and the vehicle traffic necessary to maintain them make a dent.

If anything, he said Border Patrol should be putting up more money to pay for damage. He described the harm from the border fence as "insidious," separating species from their own kind as well as food and water supplies. Though not an ideal situation, he said the mitigation money can be used to purchase land elsewhere and preserve habitat for the affected species.

"I think mitigation dollars can be put to good use," he said.

But Napolitano wrote that the tower project, which continues, is "routinely challenged with satisfying an array of environmental requirements."

"Each selected tower location may conflict with various environmental regulations or constraints, which must be addressed and/or mitigated. In addition, the relevant environmental regulations may be subject to varied interpretations depending on what level of the agency or organization is involved, which frequently leads to addition time, effort and cost to resolve before a project can proceed," the letter reads.

With the Interior Department closing off or restricting American parkland to U.S. visitors out of concern for border-related violence, some have questioned why the Border Patrol does not have better access to those areas with less cost.

Bishop has authored a bill that would restrict Interior from doing anything to "impede border security" on public lands, though the bill would not do anything about the environmental fees charged to the Border Patrol.

Jill Strait, spokeswoman for ranking Republican on the House Natural Resources Committee Rep. Doc Hastings, said it's in the Interior Department's best interest to ease those fees.

"This is taking valuable money away from Border Patrol that is supposed to be used to safeguard our nation," she said. "Border Patrol is helping to protect against environmental damage, so that should be considered appropriate mitigation in itself."