Advanced biofuels backers celebrated the U.S. Senate’s defeat Wednesday of a measure that could have derailed the military’s quest to develop cleaner alternatives to petroleum-based fuels for use in its ships and planes.

By a 62-37 vote, the Senate struck down a section of the National Defense Authorization Act that would have have kept the Defense Department from buying any alternative fuels that cost more than conventional fuels. All but two of the 37 votes for retaining the limiting language, authored by Sen. James Inhofe (R-Okla.), came from Republicans. Mark Udall (D-Colo.) led the effort to kill the Inhofe measure.

u.s. navy biofuels
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The vote doesn’t end debate on the topic – the House version of the Defense spending bill has its own biofuels prohibition – but it does remove one hurdle that the Pentagon was facing as it seeks to decrease its reliance on oil.

The development of advanced “drop-in” biofuels – cleaner-burning alternatives to conventional fuels that can go right into today’s engines without alteration – is the latest focus in an on-again, off-again U.S. pursuit of strategic alternatives to oil to fuel the military that dates back to World War II.

In 2011, at President’s Obama’s urging, the Energy, Agriculture and Navy departments entered into a memorandum of understanding to “assist the development and support of a sustainable commercial biofuels industry.” The objective, according to a Congressional Research Service report [PDF], is the “construction or retrofit of multiple domestic commercial or pre-commercial scale advanced drop-in biofuel plants and refineries.”

The cost of that three-year effort has been put at $510 million, with each department chipping in $170 million.

It didn’t take long for the political opposition to the biofuels program to stir. It started in the House in May this year when the Republican-controlled Armed Services Committee included a provision in the 2013 Defense Department budget banning the costlier alternatives, even though the Pentagon said it needed to pay a premium for the biofuels, some derived from algae oil and animal fats, to help build a biofuels supply chain that’s now in its infant stages.

Defense Secretary Leon Panetta testified that the biofuels ban “could deprive commanders of the flexibility they need to meet tactical and operational needs, and make us more exposed to potential supply disruptions and future price volatility of petroleum products.” Navy Secretary Ray Mabus pointed out, too, that the expenditures on biofuels – $12 million to purchase 450,000 gallons, for instance – have been a virtual drop in the bucket compared to the military’s outlays for conventional fuels; Mabus noted that a $1 increase in the price of oil adds $130 million to the Defense Department’s fuel costs.

Other biofuels allies, like the green-business group Environmental Entrepreneurs (E2), emphasized the economic benefits of research and development in advanced biofuels of the sort that this past summer powered the Navy’s “Great Green Fleet” in military exercises.

After Wednesday’s vote, E2’s Nicole Lederer said in a statement that “the Senate rightly stood behind America’s military with this vote, but it also stood behind American businesses.” She went on to say that military programs “are already driving innovation, private-sector investment and job creation in the biofuel industry. Now that the market has a clear signal from Washington, that growth can continue.”

A coalition of biofuels industry organization agreed, saying in a statement: “It is increasingly important to find domestically produced crude oil alternatives to improve the country’s energy security, meet global energy demands, and provide jobs, while strengthening our military and domestic industry.”