A key U.S. Senate committee that includes Sen. Susan Collins of Maine narrowly passed two measures last week that would all but end a Pentagon program that seeks to transition the military away from fossil fuels — without a vote from Collins.

Each measure passed by a single vote in a closed-door markup session of the Armed Services Committee. Collins, who has said she supports the Defense Department’s alternative fuels program, wasn’t in the room.

The situation is something of a mystery. Even in today’s polarized political climate, it is extremely unusual for senators to pass a measure intentionally in committee while an opposing member is temporarily out of the room.

Determining exactly what occurred is difficult because Senate staffers generally don’t discuss what happens in the closed-door meetings.

Collins and 25 other senators met May 24 to consider the 2013 Defense Authorization Bill. Three items in the bill relate to the Pentagon’s Operational Energy Strategy program, which came under attack by House Republicans earlier this year.

Defense Department officials introduced the alternative-energy program in June 2011 to reduce the armed forces’ dependence on oil, which they contend costs the department $20 billion each year and has resulted in the deaths of hundreds of troops and contractors escorting fuel convoys in Afghanistan and Iraq.

Navy Secretary Ray Mabus has said that increased demand for alternative fuels will help drive down the price of biofuels.

Critics, including Sen. John McCain, R-Arizona, say the program is a waste of money, because the biofuels now cost many times more per gallon than conventional fuels. Earlier this month, McCain denounced it as “a waste of taxpayer money” to promote a “green agenda” within the military.

Roll call votes show that Collins cast the decisive vote defeating an initial amendment that would have exempted the Pentagon from rules preventing federal agencies from procuring alternative fuels that produce more greenhouse gas emissions than regular fuels.

The roll call shows she did not vote on subsequent measures, to ban the purchase of alternative fuels if they are more expensive than fossil fuels they are intended to replace, and to bar the Pentagon from building a biofuel refinery without approval from Congress. Without Collins, both measures passed 13-12, a development first reported by Politico earlier this week.

Collins’ press secretary, Kevin Kelley, said that on the morning of the committee meeting in the Russell Senate Office Building, the senator got a call she had been awaiting all morning.

Capt. Bryant Fuller III, commander of the Portsmouth Naval Shipyard, called to speak with her about the fire that had burned from Wednesday evening into Thursday morning aboard the USS Miami, a nuclear-powered attack submarine.

“She had been trying to reach the shipyard and left to take the call,” Kelley said. “Those two votes were taken in her absence.”

Both measures got unanimous backing from the other Republicans on the committee. Democrats Joe Manchin of West Virginia and Jim Webb of Virginia also voted in support of them. Independent Joe Lieberman of Connecticut joined the remaining Democrats — including committee Chairman Carl Levin, of Michigan — in opposition.

“As long as there is a quorum of senators, the chairman can hold the votes following any debate,” Kelley said.

While it seems unlikely that Levin would have wanted the vote to proceed in Collins’ absence, exactly what happened is unclear. “We don’t comment on deliberations during the closed session,” said Levin’s press secretary, Kathleen Long.

A spokesperson for Sen. Jeanne Shaheen, D-N.H., also declined to comment, while the staff of McCain, the ranking Republican on the committee, did not respond at all.

Kelley said Collins intends to fight the measures when they come before the Senate in the late summer or early fall.