The US government shutdown had no drastic effect on the military, but if it remains in place everything from ship repairs to combat training will be disrupted, officials say.
With about half the Pentagon's 800,000 civilian employees placed on unpaid leave, defense officials said the military will soon face a headache trying to make do with less civilian manpower under the shutdown.
"There's going to be an impact, but it will take some time to feel the effect," said a senior military officer.
The furloughs mean that "real work doesn't get done," said the officer, who spoke on condition of anonymity.
Much of the defense department's civilian workforce are employed at bases across the country, and the military relies on them to keep equipment running and logistical networks humming.
If the shutdown drags on for weeks, planned work at shipyards and aircraft depots will have to be put off, routine administration will be neglected and some units will have to forgo training unless it is directly related to critical operations, officials said.
The shutdown came after a political impasse with Republicans in Congress tying funding for the new fiscal year to suspending or dismantling President Barack Obama's signature health care law. Obama's fellow Democrats in the Senate rejected the move and money for government operations ran out at midnight on Monday.
At the eleventh hour, Congress adopted a measure to ensure troops would get paid through the shutdown, and the Pentagon has made clear that no military operations would be affected, including the war effort in Afghanistan.
But civilians play a role in just about every military undertaking, and under the law, only some of them can be designated as "essential" to stay on the job.
As a result, military officers said they were unsure exactly how the shutdown would play out while legal advisers weighed whether a larger number of civilians could be deemed exempt from furloughs.
The last time the government shut its doors in 1995, Congress approved funding for the Defense Department. Even in that case, former commanders say the shutdown created major problems.
Paul Eaton, a retired Army major general, said he faced huge difficulties trying to prepare an armored unit to deploy to Bosnia at the time.
"The disruption based on uncertainty in funding kept us in a consistent state of turmoil," Eaton told a teleconference organized by the Truman National Security Project, a left-leaning Washington think tank.
"We didn't know if the railways were going to be able to support us...we had tanks to move," he said.
The troops made it on schedule but some planned training time had to be dropped, he said.
Eaton said the military faced an unprecedented situation with the current shutdown. "I certainly don't know and I'm not sure anybody does know what we can anticipate over the next days, weeks or months," he said.
The US Army said tuition assistance had been suspended for soldiers taking classes starting on or after Tuesday due to the shutdown. And at the military academies, many classes were called off as civilian faculty were placed on furlough.
Defense secretary Chuck Hagel, on a trip to South Korea and Japan, warned the shutdown could damage US credibility abroad and fuel anxiety among America's allies.
At the Pentagon building, there was a mood of resignation as civilians placed on leave filed out at lunch time not knowing when they would return to work. They left behind empty desks and empty spaces in the department's vast parking lot.
Many officials and senior military officers, already frustrated with automatic budget cuts, expressed disgust at the political stalemate that had created the crisis.
"We are dealing essentially with a shutdown of the Pentagon and civilian support for men and women in uniform," said one official who asked not to be named. "And this was not caused by a foreign adversary or a catastrophic natural disaster -- but it was man-made."