On Tuesday, McCain slammed the Defense Department’s “Operational Energy Strategy,” unveiled last June, as an attempt by Obama to exploit the military in order to promote his clean-energy agenda—at the expense of national security and taxpayer dollars.

“Adopting a ‘green agenda’ for national defense of course is a terrible misplacement of priorities,” McCain told National Journal Daily in an interview on Tuesday.

The administration’s first priority, he said, “is of course the defense of the nation, not a green agenda, so again, [it’s] a clear indication that the president doesn’t understand national security.”

The decorated Vietnam War veteran and 2008 Republican presidential candidate took one other punch at the Pentagon program: “It certainly is an incredible waste of taxpayers’ money that should be devoted to caring for the men and women who are serving in the military and their security needs.”

He said he intends to offer several amendments to the defense authorization bill that would slash spending on the alternative-energy programs, though he declined to describe his proposals in detail. The Armed Services Committee is expected to mark up the bill behind closed doors this week.

McCain is crafting the amendments with Sen. James Inhofe, R-Okla., who is perhaps Washington’s most vocal skeptic of climate-change science and a frequent critic of renewable-energy programs. Inhofe is the ranking member of the Senate Environment and Public Works Committee.

It’s unlikely the amendments will make it through the Democratic-controlled Senate. But McCain’s forceful and public attack on the Pentagon’s renewable-energy initiatives abruptly politicizes an issue that until now had escaped the bitter partisan fighting that surrounds most energy debates in Washington.

President Obama and military leaders, particularly Navy Secretary Ray Mabus, have presented the Pentagon energy programs—some of which predate Obama’s election in 2008—as driven purely by the goal of protecting national security and the safety of troops. That framework has until now allowed the energy initiatives to escape the scathing criticism the GOP usually directs at federal spending on clean energy.

Defense Department officials contend that the new energy initiatives are not driven by any kind of “green” agenda, but rather by the goal of reducing the military’s dependence on oil, which they say costs the Pentagon up to $20 billion annually and has led to the deaths of hundreds of troops and contractors, killed while guarding fuel convoys in Iraq and Afghanistan.

The moves, which include promoting the use of solar-powered electronics on the front line, hybrid tanks, and “smart grids” on military bases, could also increase frontline fighting power, military officials say.

But they will cost more money in the short term. For example, the Navy last year bought 150,000 gallons of algae-based biofuels from a South San Francisco company called Solazyme, and people familiar with the deal said the price was at least an order of magnitude greater than what the military pays for conventional fuel to power its jets, ships, and combat vehicles—about $3 to $4 per gallon.

In the long run, the Navy’s Mabus has argued, a scaled-up military demand for renewable energy could help drive down the price of such biofuels, and would ultimately serve to help the military strategically.

But that’s a tough argument to make even in flush times, and at the moment, the military is staring down the barrel of a mandatory $500 billion budget cut set to kick in early next year. With that in mind, McCain said he challenged Mabus over the biofuels purchase at a recent hearing. “What’s that all about when we’re having to retire cruisers early?” he said.

McCain’s attacks are mobilizing advocates of the program. One think tank, the Truman National Security Project, held a press call with retired Marine Lt. Gen. John Castellaw on Tuesday afternoon, urging Congress not to cut the energy programs.

“Moving away from oil ... ensures we remain the most capable and effective fighting force on the planet,” Castellaw said. “And that is what this is all about. This is not about politics or saving the polar bears. It is about being effective as a fighting force.”