WASHINGTON — With expectations that Congress will fail to pass a budget before the end of the fiscal year, the US Air Force's top official today sounded the warning klaxon about what impact a continuing resolution (CR) would mean for her service.

Air Force Secretary Deborah Lee James acknowledged the belief in Washington that a CR is coming, and she appears to be acting preemptively to warn members of Congress what would happen to key programs, telling reporters that as many as 60 new-start or upgrade programs could be impacted.

"Overall, a long-term CR would fund the Air Force at about $1.3 billion less than the amount we requested in FY17 and cause many, many [issues] in our system," James said.

Among the programs that could be impacted are needed upgrades to the MQ-9 Reaper unmanned system, C-130 cargo transport, and the B-52 and B-2 bomber fleets. Military construction — including needed upgrades at bases where the F-35A joint strike fighter will operate out of — would also be cut.

Newer production programs would also be impacted, James warned. She stated that the B-21 bomber would be capped, which introduces "risk" to the program's ability to deliver in the mid-2020 time frame. James also singled out the KC-46A Pegasus tanker as one which would see production capped at 12, which she warned would "delay" operational fielding of the plane.

Perhaps more concerning, James floated the idea that a CR could cause the service to break the tanker contract, which caps Pentagon costs at $4.9 billion. Prime contractor Boeing has already racked up $1.9 billion in pre-tax charges due to overruns. In 2013, the Pentagon came within 24 hours of breaking that contract due to sequestration-related budget cuts.

In the short term, James also said that production would be cut on the Joint Direct Attack Munition (JDAM) weapons, which are being used in the fight against the Islamic State group in Syria and Iraq.

"We feel that is unacceptable, particularly in light of current operation against [ISIS] and other extremists around the world," James said. However, given that munitions fall firmly under operational requirements, it may be possible for the Air Force to request a plus-up in its Overseas Contingency Operations funding for those weapons.

The question among defense experts is less whether there will be a CR and more a question of how long it will last.

Todd Harrison, a budget analyst with the Center for Strategic and International Studies, said last week that "we will almost certainly start the fiscal year in a continuing resolution yet again ... a continuing resolution that will need to stretch at least until December, so then in the lame duck session, Congress can come back, they can try to work out a budget deal at that time and then pass an omnibus appropriations bill."

However, Harrison believes that a CR would likely not roll over into the next administration.

"If we get into a continuing resolution that extends into the new administration and the new Congress, I think that's a real failure of this Congress," Harrison said "This is something they can and should be able to resolve by the end of this calendar year."

Twitter: @AaronMehta