The decisions deal a particular blow to Puerto Rico, which stands to see more than $400 million worth of planned projects lose funding. Roughly $770 million of the money will be taken from projects in allied European nations aimed at helping them deter a possible attack from Russia.

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Officially, the Pentagon is saying the affected projects are “deferred,” but in order for them to go ahead in the future, Congress must again fund them. The Republican-led Senate has agreed to do so in its annual defense policy bill, but the Democratic-led House refused in its version of the bill. The two sides will negotiate a possible compromise in conference, the period when the Senate and House make trades to meld two bills into one before seeking the president’s signature.

If Congress declines to fund the construction projects, they will remain in limbo and effectively be defunded. If they are indeed “backfilled” in the coming year’s budget, some could proceed without delay, because the Pentagon deliberately chose projects with contract award dates scheduled for future years. The department also chose projects that were already facing delays.

Rep. Mac Thornberry (R-Tex.), the top Republican on the House Armed Services Committee, argued that Trump had been “forced” to reroute funding away from military projects toward efforts to stem the migration crisis at the border, and he urged Congress to restore the money.

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“Failing to do so only forces our troops to pay for political discord in Washington,” Thornberry said in statement Wednesday.

But Democratic lawmakers vowed again this week not to backfill funds for the affected military projects — arguing that Congress already approved the money once and would not do so again.

“The president is ignoring his lack of authority when it comes to stealing congressionally directed funding,” Rep. Ben Ray Luján (D-N.M.) said in an interview Wednesday. “The notion that the president is suggesting that, ‘Well, don’t worry, the projects will be backfilled,’ just shows the lack of understanding from this president of how the appropriations process works.”

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Luján represents Holloman Air Force Base, which stands to lose $85 million that had been designated for a facility holding a squadron for MQ-9 Reaper drones. Holloman had been chosen a decade ago as a preferred base for the squadron, Luján said.

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“This is a facility that would house training units for new pilots and sensor operators,” Luján said. “This is an essential part of our national security.”

The Pentagon’s disclosures of the affected projects also prompted objections from Republicans, including Sens. Mike Lee and Mitt Romney of Utah, which will lose $54 million of money allocated for Hill Air Force Base.

“Funding the border wall is an important priority,” Romney said in a statement. “The Executive Branch should use the appropriate channels in Congress, rather than divert already appropriated funding away from military construction projects and therefore undermining military readiness.”

Lee and Romney voted against Trump’s border emergency in March.

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A senior defense official, speaking on the condition of anonymity at a Pentagon briefing on Wednesday because the Defense Department declined to hold the event on the record, said the agency is committed to proceeding with the projects on the list and plans to work with Congress to replenish their funding. The official expressed confidence that the funding would be backfilled but acknowledged it was not guaranteed.

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The official said that of the 13 projects on the list from Puerto Rico and the U.S. Virgin Islands, 10 were part of efforts to restore military installations after Hurricane Maria. The projects include the construction of a school for military children on what was once Ramey Air Force Base and improvements to Camp Santiago, a training facility operated by the Puerto Rico National Guard.

The official said the contracts on those projects are not due to start for at least a year, which gives Congress an opportunity to restore the funding and proceed without delay.

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“We are fully committed to the recovery effort for Maria,” the defense official said.

The administration is also asking allies to foot the bill for some of the projects on foreign soil, the official said. Those include more than $770 million worth of projects for the European Deterrence Initiative and its predecessor program, which President Barack Obama launched in 2014 to shore up the defenses of European allies after Russia annexed Crimea from Ukraine.

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The affected initiatives include a plan to build a facility for special operations forces and their training in Estonia, projects to construct ammunition and fuel storage facilities and staging areas in Poland, and planned upgrades to surveillance aircraft facilities in Italy, as well as airfield and fuel storage upgrades in Slovakia and Hungary.

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More broadly, the list of projects ranges the gamut, from a space control facility at Peterson Air Force Base in Colorado; to weapons training ranges in Mississippi, Oregon, Oklahoma, Wisconsin and Alaska; to central heat and power plant boilers that need repairs at Eielson Air Force Base in Alaska. Also on the list is a $9 million plan to replace a working-dog treatment facility at Guantanamo Bay in Cuba.

Nine projects involve renovating and replacing schools for military children on bases in the United States and abroad. Asked why the Pentagon was prioritizing border barriers over education facilities for the children of military families, the senior defense official said, “We have existing facilities for ongoing superior education that the Department of Defense provides through its schools — and that will continue until we get these projects built.”

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The information about the projects comes a day after Defense Secretary Mark T. Esper formally approved a decision to divert the $3.6 billion to pay for 175 miles of barrier on the southern border.

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To do so, Esper relied on an obscure part of the U.S. code governing the military. Known as Section 2808, the law allows the defense secretary, during national emergencies requiring the use of the armed forces, to tap military construction funds without sign-off from Congress for projects necessary to support those troops. Esper deemed the barriers necessary to support the troops Trump deployed to the border to help Customs and Border Protection with an influx of primarily Central American migrant families.

“These projects will deter illegal entry, increase the vanishing time of those illegally crossing the border, and channel migrants to ports of entry,” Esper wrote in his determination. “They will reduce the demand for [Department of Defense] personnel and assets at the locations where the barriers are constructed and allow the redeployment of DoD personnel and assets to other high-traffic areas on the border without barriers.”

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The Pentagon gained access to the authority after Trump declared a national emergency in mid-February, having failed to persuade Congress to provide more money for the project. The dispute led to the longest U.S. government shutdown in history, lasting 35 days in late 2018 and early 2019.

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The Trump administration has also used a separate counterdrug law to access $2.5 billion for barrier construction from the Pentagon budget. It is also taking $601 million from the Treasury Department asset forfeiture fund for the barrier construction. On the campaign trail, Trump regularly said Mexico would pay for his border wall project.

The $3.6 billion will pay to replace existing barriers or fences and construct new fence systems.

Some $1.16 billion of the funding will go to construct a second fence system to prevent pedestrian entry where the military’s Barry M. Goldwater Bombing Range abuts the border with Mexico and to replace vehicle barriers that separate the Cabeza Prieta National Wildlife Refuge from Mexico with fencing. An additional $40 million will go toward replacing a 1.5-to-2-mile stretch of fencing along the bombing range.

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An additional $1.27 billion will be spent on a new fence system for about 52 miles along the Rio Grande outside Laredo, Tex. And $476 million will go to replace 23.5 miles of vehicle barriers with fencing in Hidalgo and Luna counties in New Mexico.