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President Donald Trump decided to shift military funds to build the southern border wall last month despite warnings from top Pentagon officials who cautioned that doing so could hurt the Defense Department long-term, Acting Defense Secretary Patrick Shanahan said Tuesday.

Shanahan told lawmakers on the House Armed Services Committee that the President opted to move forward with the plan after being informed it would likely cause the Pentagon to lose “what amounts to a privilege,” when it comes to its ability to re-program certain funding without formally seeking congressional approval to do so.

Prior to the emergency declaration, “we said here are the risks to the department long term and those risks were weighed,” Shanahan said, adding that the Pentagon is executing a “legal order from the commander in chief.”

The Pentagon notified Congress Monday night that it authorized the transfer of $1 billion to begin new wall construction along the US-Mexico border, drawing immediate objections from Democratic lawmakers.

A Pentagon budget reprogramming notification sent to Capitol Hill on Monday and obtained by CNN indicates that up to $1 billion will go toward building 57 miles of fencing, improving roads and other measures on the southern border.

Shanahan gave approval the Army Corps of Engineers to begin planning and construction for the project Monday night as the Pentagon notified congress

The department will direct the funds toward 18-foot-high fencing along the Yuma and El Paso sections of the border, according to a letter Shanahan sent to Secretary of Homeland Security Kirstjen Nielsen.

In February, Trump declared a national emergency in order to funnel billions of dollars to wall construction. As part of his announcement, he directed the use of counterdrug monies to partially fund new wall construction. Under the national emergency, other funds can also be dedicated to building the wall and related infrastructure, including military construction funds.

Monday’s announcement was just the first $1 billion the administration is making available for wall funding. The administration said previously it plans to shift an additional $1.5 billion at some point in the future.

These initial counterdrug funds will ultimately flow from the Department of Homeland Security to the Army Corps of Engineers to begin construction.

“It was a very difficult discussion and we understand the significant downsides of losing what amounts to a privilege. The conversation took place prior to the declaration of a national emergency, it was part of the consulting that went on,” Shanahan told lawmakers on Tuesday.

Shanahan also recognized that the Pentagon would lose some budget flexibility it has previously enjoyed as the department examines how it will deal with funding construction for portions of the wall that come under the purview of the Pentagon.

The House Armed Services Committee sent a letter to the Defense Department Tuesday saying it has denied the Pentagon’s reprogramming request.

“The committee does not approve the proposed use of Department of Defense funds to construct additional physical barriers and roads or install lighting in the vicinity of the United States border,” the bipartisan letter states.

Sen. Jack Reed, the top Democrat on the Senate Armed Services Committee, said there’s nothing Congress can do to stop the Pentagon from legal transferring as much as $4 billion across budget accounts.

But in the past, he said, the Pentagon would notify the congressional defense committees about the reprogramming, and if the committees objected they wouldn’t move forward with the transfer. In this case, however, the Pentagon is ignoring Congress, which is likely to spark changes to the reprogramming laws going forward, as House Armed Services Committee chairman, Democrat Rep. Adam Smith alluded to on Tuesday.

Shanahan told reporters Tuesday that he has received the memo from Smith but has not reviewed its contents.

“I got that memo today. We’ll take a look and see what that means,” he said.

CNN’s Jeremy Herb, Ryan Browne and Jamie Crawford contributed reporting.