WASHINGTON ― The Pentagon isn’t facing a government shutdown, thanks to an emergency budget extension passed Thursday. But that doesn’t mean top officials are without budget worries.

That’s because the short-term budget deal approved by Congress, known as a continuing resolution, freezes billions of dollars in planned Pentagon acquisition programs, as well as some of President Joe Biden’s top priorities to deter China. It could be months before they move ahead.

The continuing resolution runs from the start of the fiscal year, Oct. 1, through Dec. 3, which gives Congress nine more weeks to pass a fiscal 2022 budget plan for the military and the rest of the federal government. However, it also stalls “new-start” programs and production increases, since all budget lines simply continue at the previous year’s level.

Exceptions can be made for “anomalies.” But for now, the continuing resolution means a Pentagon priority — a $5.5 billion boost for the development and testing of cutting-edge technologies that could deter China — is on hold.

“There’s no goodness with a CR,” Rear Adm. John Gumbleton, the deputy assistant secretary of the Navy for budget, said at a public forum in August.

Navy officials say a CR freezes $8 billion for new equipment spending, $2.5 billion in operations and maintenance activities and $2 billion for personnel.

Delays would hit the Air Force’s 16 new-start procurements, which comprise $2.3 billion of its 2022 budget request. Among the efforts on hold would be a $300 million initiative to develop cutting-edge hypersonic weapons, as well as production increases for the F-15′s Eagle Passive Active Warning Survivability System and the Small Diameter Bomb II, among others.

“CRs immediately disrupt major exercises and training events, impede readiness, delay maintenance, impose uncertainty on the workforce, curtail hiring and recruitment actions, and induce inefficient and constrained contracting practices,” Air Force spokesman Capt. Jacob Bailey said. “CRs delay the implementation of new technology development in support of national security priorities.”

The fledgling Space Force is especially sensitive to continuing resolutions. Chief of Space Operations Gen. John “Jay” Raymond said a CR would delay plans to transfer hundreds of Army and Navy billets as well as certain satellite communications capabilities, mission responsibilities and related funding to the new service.

“All those capabilities, all those systems on-orbit, plus the ground stations that operate those capabilities and integrate those capabilities ― that all transfers over to the Space Force, beginning 1 October,” Raymond said Monday at a Defense One conference. “If there is a continuing resolution, we have to wait until that is resolved.”

The Navy budget requested $4.6 billion to continue building the first Columbia ballistic missile submarine, but service officials have voiced worries the program could be knocked off track by a CR. On the other hand, the program schedules for the naval aircraft and the Arleigh Burke-class destroyers allow for some leeway, they said.

“I’m always worried about Columbia, although I don’t think it needs money in the first two months. But if we get to a second CR I think we would have to do something there,” said Jay Stefany, the acting assistant secretary of the Navy for research, development and acquisition.

But while Pentagon officials complain of CR pain, a recent Government Accountability Office report found they have actually found ways to cope with the constraints. GAO’s recent review of several major defense acquisition programs couldn’t find any of the delays and cost overruns that are expected to result from CR-related funding hiccups.

For example, the Army raised concerns in 2017 that its new Armored Multi-Purpose Vehicle program would be delayed by a CR, but officials adapted by pushing a decision to go into production until after regular spending legislation was enacted for fiscal 2018. (The compressed fiscal year did mean the Army had to buy fewer AMPVs than it planned.)

“When we met with officials from these programs, we learned that while the Selected Acquisition Reports speculated that CRs could have resulted in program delays or cost increases, in actuality, the CRs did not affect the programs,” GAO’s Sept. 14 report reads.

The services often postpone service contract start dates and nonessential purchases or training to later in the fiscal year, though defense officials told GAO it can be hard to manage contracts and buy equipment when they don’t know what level of funding they’ll get.

The CR includes only a few exceptions or “anomalies” for the Pentagon, including $885 million for the Air Force’s program to buy commercial microelectronic equipment, while another would protect a program to develop jam-resistant GPS equipment.

The White House requested those items along with $6.3 billion in emergency funding to resettle Afghan refugees and $895 million to repair Navy and Air Force facilities damaged by natural disasters.

It would be atypical for Congress to include more than a handful of anomalies for DoD. Over the last 10 years, the Pentagon has asked Congress to include funding for as few as 36 anomalies and as many as 154, but it’s received an average of four each year.

Adding anomalies is a balancing act, said Todd Harrison, director of defense budget analysis at the Center for Strategic and International Studies. If the administration got all the anomalies it requested, that would reduce much of the pain a CR causes and give Congress less of an incentive to pass a final appropriations bill for the year.

“The anomalies you normally see proposed by the White House are the programs and activities that are higher priority and more subject to disruption,” Harrison said.

The Defense Department has adapted such that CRs tend to be “just a bit of a bureaucratic headache” ― so long as the stopgap measures don’t go beyond six months, Harrison said. Over the last 60 years, defense has started the fiscal year on a continuing resolution 80 percent of the time.

Will Congress stay deadlocked on the federal budget into February? Harrison said it’s too soon to say, but Congress must first has to address its other high profile impasses, over the country’s borrowing limit and massive packages of spending on infrastructure and other domestic priorities for Democrats.

“The longer they remain stuck on those things, the longer this CR will ultimately be,” Harrison said.

Rachel S. Cohen and Leo Shane III contributed to this report.

Joe Gould was the senior Pentagon reporter for Defense News, covering the intersection of national security policy, politics and the defense industry. He had previously served as Congress reporter.

Megan Eckstein is the naval warfare reporter at Defense News. She has covered military news since 2009, with a focus on U.S. Navy and Marine Corps operations, acquisition programs and budgets. She has reported from four geographic fleets and is happiest when she’s filing stories from a ship. Megan is a University of Maryland alumna.

Jen Judson is an award-winning journalist covering land warfare for Defense News. She has also worked for Politico and Inside Defense. She holds a Master of Science degree in journalism from Boston University and a Bachelor of Arts degree from Kenyon College.

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