The budget the Defense Department submitted for 2016 aims to let the military begin to dig out from billions of dollars in deferred facility maintenance caused by two prior years of sudden spending cuts. But Pentagon officials freely acknowledged Tuesday that even their own proposal isn’t a complete solution to neglected infrastructure, and relies largely on the hope that Congress will waive the defense funding caps it has already passed.

DoD’s overall budget proposal would bust the Budget Control Act’s spending limits by $35 billion in 2016, and some of the extra funding would be used to partially restore the facility sustainment, restoration and modernization programs that were slashed by one-third in 2015.

But the Pentagon proposal would still only provide 81 percent of the funds the military services say they need to adequately maintain existing buildings and other base infrastructure. Put another way, even if DoD gets another reprieve from sequestration, its facilities will once again get the short end of the stick, and if it doesn’t, things will be even worse.

“Facility sustainment is still the place where I see the highest risk,” said John Conger, DoD’s acting assistant secretary for energy, installations and environment.

“We have a new model that tells us how much we should be allocating to preventative maintenance and an internal policy that we should fund 90 percent of that, and we don’t. But last year it was closer to 70 percent. We need to make some progress, because it’s cheaper to do preventative maintenance than to repair critical problems, and it’s cheaper to repair critical problems than to replace a facility. If you stop funding the preventative maintenance at the front, you’re going to suck up all of your funding with critical repairs, and eventually you’re going to have to replace the buildings.”

Delayed maintenance has already left the military with plenty of buildings that are in rough shape, officials told the House Appropriations Committee Tuesday. Under the department’s rating system, called the Facility Condition Index, 24 percent of its overall inventory is already categorized as in “poor” condition and another 7 percent meets the criteria for a “failing” building.

DoD created the 90 percent maintenance goal in order to develop a multi-year plan to improve its building inventory, including repairing or replacing buildings and demolishing those that are beyond hope.

But Dennis McGinn, the assistant secretary of the Navy for energy, installations and environment, emphasized that the 2016 budget — if approved by Congress — would only be the beginning of a long catch-up process.

“We are funding the maintenance of our facilities at a level that arrests the immediate decline in the overall condition of our most critical infrastructure,” he said.

“By deferring less-critical repairs, we do acknowledge that we are allowing certain facilities to degrade. However, this budget has us headed back in the right direction. Last year’s funding cuts, if continued into the future, would have led to a rapid degradation in our overall shore establishment readiness.”

But even decisions to defer repairs that might seem not-so-critical at one moment have a tendency to lead to sudden and unexpected maintenance emergencies.

Last year, a 15-foot sinkhole suddenly opened on the primary runway at the naval air station in Jacksonville, Florida, taking it out of commission and forcing the Navy to issue an emergency solicitation for what turned out to be $52 million in emergency repairs. The sinkhole was not an act of nature.

“The root cause was a failing sewer pipe under the runway,” McGinn said. “The replacement of that infrastructure and the reconstruction of the runway had been on our military construction list for many, many years. We’re doing it now, of course, but that’s one example of how the failure to do the necessary maintenance and sustainment adds more risk. We have to watch those things very carefully and do our best to put the money where we think it’s going to do the most good.”

The DoD budget also requests a substantial increase in military construction funding — 29 percent more than last year — even at a time when the military is shrinking.

Part of the difference is explained by the fact that the department also scaled back on new construction last year in response to sequestration, and is now trying to catch up.

But Katherine Hammack, the assistant secretary of the Army for installations, energy and environment, said the bill for new construction is likely to grow in future years as existing facilities continue to approach failing conditions.

“In the Army, the results of not paying for sustainment in 2013 and 2014 means that we now have a $3 billion maintenance backlog and 5,500 major work orders,” she said.

“If you can’t sustain a facility right, it progresses toward a restoration and modernization issue. And if you don’t get after that, soon enough, the facility becomes failing. As we continue to underfund sustainment, we increase MILCON requirements down the road.”

While officials acknowledge that their own funding plan would not solve the problem of deteriorating infrastructure, they say a return to sequestration will almost certainly make it worse. In the big picture, cuts to facility maintenance are relatively easy choices both in the Pentagon and on Capitol Hill compared with eliminating weapons platforms or reducing end strength, so base upkeep is likely to continue to get shorted again if there are further cuts to be made.

“To put it very simply, the BCA would require us to make more no-win decisions between all of our construction and sustainment projects,” said Miranda Ballentine, the Air Force’s assistant secretary for installations, environment and energy. “The Air Force has knowingly underfunded mission-critical infrastructure over the last several years, including nuclear infrastructure, space infrastructure and in particular, existing mission infrastructure. Our budget proposal allows us to begin to chip away at that problem.”

The military’s bills for facility upkeep are also driven by the fact that their scarce maintenance dollars are spread across a real estate portfolio that’s much larger than what the Pentagon believes it needs.

While the Navy thinks its facilities are matched just about evenly with its existing size, recent assessments from the other services say the Army has 18 percent excess capacity; the Air Force has 30 percent more than necessary.

“There’s more we can do to improve the affordability and viability of our installations, which today are simply too old, too big and too expensive,” Ballentine said.

Congress has shot down DoD’s requests for another round of base realignments and closures for several consecutive years, citing the high costs of the last round in 2005. The Pentagon continues to insist that a new round would be different since it would be conducted at a time when the military is shrinking instead of growing, and would be explicitly designed to save money rather than transforming the military’s stateside footprint.

Final decisions on base closures would be up to an independent commission, but DoD would be able to provide its own input. Officials believe they could achieve $2 billion in annual cost reductions by divesting around 5 percent of the military’s current base infrastructure.

Conger said his staff has been honing its skills to determine exactly how it would make those recommendations without cutting back on military capability, including through the round of European base closures the department announced in January.

“The European Infrastructure Consolidation process we just went through is a great example,” he said. “We used it as a test drive for a lot of staff that had never been through a BRAC before. We made a very clear choice not to reduce any operational capability or reduce our ability to deal with a conflict in the region. That’s what drove the process in Europe, and we expect the same thing from a BRAC round.”

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