David Riggs, a fuel operator with the Fleet Logistic Center Puget Sound Manchester Fuel Department, prepares to deliver biofuels to the U.S.N.S. Henry J. Kaiser during the Great Green Fleet demonstration. Photo: U.S. Navy

The Navy’s plans to power warships with biofuels may not be out of gas quite yet. On Tuesday, the Senate defense appropriations subcommittee voted to continue funding the alternative energy program, keeping alive the Navy’s push for an ambitious “Great Green Fleet,” propelled by renewable fuels.

“I think we do have the funding for that,” Sen. Daniel Inouye said. Inouye, the defense committee chairman, is one of the Senate’s most powerful voices on military. matters According to a summary provided by the subcommittee, the defense bill includes “increases” to alternative energy programs (.pdf). But the complete dollar amount won’t likely be revealed before Thursday.

Another fight can also be expected starting Thursday, as the green fuel funding — part of the $604 billion defense budget for fiscal year 2013 — next moves on to the full Senate Committee on Appropriations for a vote. But Senate Democrats who support the program and control a majority of seats, hope to alter any potential changes before a full vote, according to Reuters. In any case, it’s a lifeline for a program that nearly imploded in May, when the House and Senate defense committees restricted spending for military biofuels.

On the line is one of the top priorites for Navy Secretary Ray Mabus, who has developed an ambitious program to use biofuels and other renewables for half of the Navy’s energy needs by 2020. The biofueled Great Green Fleet, as its called, sailed out on its first demonstration voyage in June.

But Republicans have used the biofuel program as a way to hit the White House. Critics have charged the Navy is moving forward on an ambitious and costly — potentially $1.76 billion per year — alternative energy program when a looming budget freeze threatened to cut funding to new ships and planes.

“You are the Secretary of the Navy, not the Secretary of Energy,” Sen. John McCain wrote in a letter to Mabus on Friday. “I strongly encourage you to marshal the time and resources of your team to avert serious threats to the core missions and capabilities of the Department of the Navy, instead of spending defense dollars to advocate for your view of our national energy priorities.”

Mabus, and allies such as Deputy Assistant Secretary of the Navy for Energy Tom Hicks, accept the biofuels won’t be cheap — at first. But say these costs are temporary, and that “the $1.8 billion figure assumes oil prices won’t be higher in 2020, and that biofuel costs won’t go down,” Hicks wrote in an op-ed for Danger Room on Friday.

With yesterday’s vote, and if the Navy’s biofuel buys clears its coming Senate hurdles, we may have a chance to find out.

Updated: The post incorrectly stated the bill would next go to the Senate Armed Services Committee. In fact, the vote next moves to the Senate Committee on Appropriations.