Proposed limitations on the Pentagon’s controversial alternative-fuel development efforts added to the Senate Armed Services Committee’s (SASC) new defense bill only narrowly passed the panel and were opposed by its chairman.

The SASC’s fiscal year 2013 defense authorization bill largely prohibits the Pentagon from buying alternative fuels if they cost more than traditional fossil fuels and also bans the Pentagon from building a biofuels refinery unless specifically authorized by law.

These two prohibitions were supported last week in the SASC’s closed-door markup of the defense authorization bill by SASC Ranking Member John McCain (R-Ariz.) but opposed by Chairman Carl Levin (D-Mich.). The provisions both were adopted via 13-12 votes of the committee, according to a tally of roll call votes.

McCain, who touted the biofuels changes to reporters after the SASC approved the bill last Thursday, has been among the congressional critics–largely Republicans–of the Navy’s work to create a commercially viable biofuel market. At a March 15 SASC hearing he lamented that in 2008 the Navy paid $424 per gallon for 20,000 gallons of biodiesel made from algae.

“I will seek to act on amendments on the floor to try to prevent this kind of waste of the taxpayers’ dollars, where they’ve paid $424 a gallon for algae fuels,” McCain told Navy Secretary Ray Mabus at the time.

Mabus countered that the military’s biofuels costs have been cut in half and he is “convinced that as the military brings a market here that the cost of biofuels will be competitive with existing fossil fuels.”

The senator slammed the navy for spending $170 million on the biofuel effort with the departments of Energy and Agriculture, saying “it’s the Energy Department who should be doing that.”

In the House, Armed Services Readiness subcommittee Chairman Randy Forbes (R-Va.) has been a vocal critic of the Pentagon’s alternative-energy efforts, telling Mabus he is not the energy secretary.

Mabus has maintained that Navy cannot afford to remain dependent on foreign sources of fuel.

The Air Force has also worked on developing biofuels for its aircraft.

Levin has defended the military’s alternative-energy efforts, and voted against the two provisions included in his committee’s defense authorization bill.

The alternative-fuel provision calls for prohibiting “the use of funds authorized to be appropriated to the Department of Defense in FY 2013 from being obligated or expended for the production or sole purchase of an alternative fuel if the cost exceeds the cost of traditional fossil fuels used for the same purpose, except for continued testing purposes,” according to the SASC.

The biofuels-refinery language would “prohibit the construction of a biofuels refinery or any other facility or infrastructure used to refine biofuels unless the requirement is specifically authorized by law.”

The 12 senators who joined McCain in voting to add the provisions to the SASC bill are Sens. Jim Webb (D-Va.), Joe Manchin (D-W.Va.), James Inhofe (R-Okla.), Jeff Sessions (R-Ala.), Saxby Chambliss (R-Ga.), Roger Wicker (R-Miss.), Scott Brown (R-Mass.), Rob Portman (R-Ohio), Kelly Ayotte (R-N.H.), Lindsey Graham (R-S.C.), John Cornyn (R-Texas), and David Vitter (R-La.).

The 11 senators who voted with Levin in opposing the alternative-energy language now in the bill are Sens. Joseph Lieberman (I/D-Conn.), Jack Reed (D-R.I.), Daniel Akaka (D-Hawaii), Ben Nelson (D-Neb.), Claire McCaskill (D-Mo.), Mark Udall (D-Colo.), Kay Hagan (D-N.C.), Mark Begich (D-Alaska), Jeanne Shaheen (D-N.H.), Kirsten Gillibrand (D-N.Y.), and Richard Blumenthal (D-Conn.).