Sen. John McCain (R-Ariz.) is carrying his fight over Defense Department spending to a new level — the structure of Congress itself.

Last week, I wrote that his initial target was the culture of Pentagon officials who have “been inclined to lose sight of affordability as a goal and just reached for more money as a solution to most problems.”

His newest quarry: The Senate Appropriations Committee. Or as he put it Wednesday in a Senate floor speech, “a handful of senior appropriators and their unelected staffs [who] dictate the spending of hundreds of billions of dollars — often in a manner that directly contravenes the will of those committees that still authorize spending.”

There has always been tension in the archaic, two-step way Congress approves money for executive departments. House and Senate authorizing committees approve programs and set budget levels, and then the “powerful” House and Senate appropriations committees approve the actual figures, sometimes lower than that authorized.

In recent years, however, with Congress unable to pass authorizing bills on time and the advent of “omnibus” spending bills, appropriators have taken to moving funds around, including adding money for projects not specifically authorized.

McCain is the ranking Republican on the Senate Armed Services Committee, which hasn’t brought its final version of the fiscal 2012 defense authorization bill to the Senate floor. That’s because the debt-limit agreement requires an additional spending reduction in fiscal 2012, which the panel has yet to make.

Meanwhile, the Senate Appropriations Committee on Sept. 15 approved its version of the legislation.

McCain said the appropriators used “budget gimmicks totaling over $10 billion to mislead the American people about the savings the committee claims to achieve.”

According to McCain, the “core” Defense Department budget was set at $513 billion for fiscal 2012, the same figure as approved for the current year.

There is another pot of money for the Pentagon that is considered “emergency spending” and “off budget.” It funds the fighting in Afghanistan and Iraq. For fiscal 2012, that figure was set at $117 billion.

The committee’s “gimmick,” according to McCain, was to cut $10 billion from this war account, partly based on “a presumption of decreased troop strength in Iraq and Afghanistan.” McCain pointed out that assumes reductions go as planned and that there is no need to keep additional troops in Iraq after Dec. 31.

But then, the committee shifted $10 billion in programs from the “core” budget to the war account. Among the programs shifted were $4 billion for Army, Navy, Marine and Air Force service depot maintenance and $1.5 billion for procurement of unmanned aircraft for the Air Force, Army and Navy.

That shifted $10 billion made up nearly half of the $26 billion the committee claimed to have cut from President Obama’s core Defense Department request.

But, according to McCain, the committee “still found money for over $2.3 billion in additional spending not requested by the Department of Defense and for items that are far from real Defense requirements.” These included rewards to special interests and funds for members’ pet projects,McCain said.

He pointed out $33 million in operations and maintenance funds “to purchase school buses, to build phase one of a repository for cultural artifacts, and funding for a mental health substance abuse facility on Guam.” This money, and some $40 million next year to finish these programs, is designed to help secure Guam’s cooperation in a plan to move 8,700 Marines and their 9,000 dependents from bases in Okinawa.

The costs of this move keep rising. It is now between $18 billion and $23 billion, and the Senate Armed Services panel and others have halted construction funds until less-expensive alternatives or a complete master plan is offered.

McCain also went after the $354 million for peer-reviewed medical research added by the Senate committee, as it has been by Congress for 19 years. Called the Congressionally Directed Medical Research Programs, the initiative has grown from the first year’s $25 million for breast cancer research. It requires contractors to run almost every major aspect of the program, which includes research for ovarian and prostate cancers.

McCain doesn’t question its overall merit, but whether it “diverts critical resources away from our men and women in harm’s way.”

McCain is not alone. In March, Rep. Mac Thornberry (R-Tex.), chairman of the House Armed Services Committee’s subcommittee on emerging threats, questioned whether Pentagon medical research on cancer should remain a priority at a time of tightened budgets. Thornberry noted that much of the research has a “tenuous connection to the warfighter or even our service people” and that funding had been “foisted upon the department by Congress.”

Wearing his Armed Services hat, McCain pointed out some $850 million in reductions his committee had made that the appropriations panel passed up. And he listed $675 million that neither the Pentagon had sought nor his committee authorized.

Finally, McCain mentioned a handful of small additions by the appropriation committee for youth programs, including $5 million for the National Guard Youth Challenge, that were meritorious but examples of tasks assumed during flusher times.

I am only sorry the senator didn’t list reducing the $325 million to be spent on military bands next year. The House Armed Services Committee cut $125 million in its version of the fiscal 2012 defense authorization bill, and the full House approved the decision. That’s one instance where House authorizers made a good choice.

There is still time for McCain to support them when that bill hits the Senate floor.