Updated Nov. 29, 2016, at 4:29 p.m. EST with congressional comment.

WASHINGTON — Secretary of Defense Ash Carter on Tuesday blasted a congressional plan for an extended continuing resolution that could last until May, calling it "unprecedented and unacceptable" in a letter to Capitol Hill -- one that has some staffers in Congress scratching their heads. 

The letter, addressed to Speaker of the House Paul Ryan and Senate Majority Leader Mitch McConnell, notes that the government has "never" operated under a CR through a presidential transition, nor had one that lasts this long.

"I am particularly troubled by information that Congress may be considering a CR through May. A short-term CR is bad enough, but a CR through May means [the Department of Defense] would have to operate under its constraints for two-thirds of the fiscal year. This is unprecedented and unacceptable, especially when we have so many troops operating in harm's way," Carter wrote. "I strongly urge Congress to reject this approach."

See Carter's letter to Speaker Paul Ryan and Majority Leader Mitch McConnell

The threat of a CR going until May is news, as indications before the Thanksgiving break was that a CR was coming, but one that would last only until March or April. Staffers from both the House and Senate sides expressed confusion about Carter's claim of a CR lasting that long, with some indicating they believed the Secretary misinterpreted a plan for the CR to last until the end of March.

However, a senior Pentagon official, speaking on background, pushed back at that idea and said the building was aware of discussion about a longer CR. 

"If they are no longer talking about May, that would be welcome news to us," the official said.

In an unusual move, the existence of the letter was announced by Pentagon Press Secretary Peter Cook. Such letters are usually revealed only when leaked from the Hill.

Asked why the Pentagon made the existence of the letter public, Cook said it underlined Carter’s concern over the potential CR.

"We got word there was a risk, a possibility of an extended CR. There is obviously a limited time that Congress is here to take action on these matters, so the secretary felt time was of the essence," Cook said. "Because of that, he felt it was important to send this message out and deliver what he felt was his view on this issue."

In the letter, Carter outlined the biggest concerns with such a long CR, including the operations and munitions accounts and that the capping of the European Reassurance Initiative, which is planned to increase fourfold in fiscal 2017, would be stuck at FY16 levels.

"In addition, a CR denies DoD the authority to start new programs, increase production rates, or initiate multi-year procurement, each of which are critical to securing the capabilities and capacity to execute the national defense strategy," Carter wrote. "In FY17 alone we need 57 new starts and 86 production increases, all of which would be delayed for the duration of a CR. As a result, the CR would undermine critical programs such as the KC-46 Tanker, Apache and Blackhawk helicopter procurements, and the Ohio Replacement submarine. Failure to continue these programs as planned will cost the taxpayer hundreds of millions of dollars in needless contractual penalties."

Leo Shane of MilitaryTimes contributed to this story.

Aaron Mehta was deputy editor and senior Pentagon correspondent for Defense News, covering policy, strategy and acquisition at the highest levels of the Defense Department and its international partners.

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