WASHINGTON (Reuters) - U.S. Secretary of Defense Ash Carter voiced opposition to extending a temporary government funding bill well into next year, saying it would negatively impact the military, including in the fight against Islamic State.

Washington has been operating since Oct. 1 under a stopgap spending bill, known as a “continuing resolution,” to keep most federal programs running. It expires on Dec. 9. House and Senate leaders are negotiating the end date for a new temporary funding bill.

"The most problematic shortfalls DoD (Department of Defense) will face in a long-term CR (continuing resolution) are in the operations and munitions accounts that fund counterterrorism operations and assistance in Afghanistan, Iraq and Syria, among other priorities," Carter wrote in the letter to top Congressional leaders.

Carter said the Pentagon had never been under such a situation during a presidential transition, calling it "unprecedented and unacceptable."

(Reporting by Idrees Ali; Editing by Chris Reese)