ABILENE, Kansas (Reuters) - Defense Secretary Robert Gates told the U.S. military on Saturday it must rein in spending that he called out of sync with today’s tough economic times, and said budget woes could be a factor in deciding whether to use force against Iran and others.

Defense Secretary Robert Gates discusses changes to the Pentagon's "Don't Ask, Don't Tell" policy prohibiting homosexuals from serving openly in the U.S. military during a media briefing in the Pentagon Briefing Room in Washington, March 25, 2010. REUTERS/Hyungwon Kang

Promising to play a hands-on role in wringing out savings, Gates held out the possibility of axing headquarters, merging whole agencies and culling the officer corps, taking on entrenched interests sure to put up a fight.

Sticker shock from wars in Afghanistan and Iraq also mean President Barack Obama and Congress may be more cautious about committing U.S. forces to another costly military engagement, he said.

“I do think that as we look to the future, particularly for the next couple of years or so while we’re in Iraq and Afghanistan, I think the Congress and the president would look long and hard at another military operation that would cost us $100 billion a year,” Gates told reporters.

“If there’s a real threat out there, the president and Congress will spend whatever it takes to protect the nation. But in situations where there are real choices, I think this would be a factor,” he added.

Asked if Iran fell into the category where costs would be a factor in deciding whether to strike over its nuclear program, Gates said it was unclear. “It depends on developments over the next year or two,” he said.

Gates said his goal was to cut overhead in the Defense Department’s nearly $550 billion baseline budget between two to three percent, or $10 billion to $15 billion per year, starting in fiscal 2012. The savings would allow the Pentagon to sustain force levels and free up funds for modernization programs.

Without such savings, Gates said, “it is highly unlikely that we will achieve the real growth rates necessary to sustain the current force structure.”

The budget warning was widely seen as part of stepped up efforts by Gates to define his legacy as Pentagon chief.

The venue Gates chose to deliver his message was the presidential library of Dwight D. Eisenhower, who warned about a “military-industrial complex” in a January 17, 1961, farewell speech.

‘ROOT-AND-BRANCH’ CHANGES

High unemployment and a record $1.4 trillion budget deficit are among the toughest domestic challenges Obama faces and could dim prospects for his Democratic Party in congressional elections in November.

Gates said the military spending “gusher” sparked by the September 11, 2001 attacks on the United States “has been turned off.” He cited America’s “difficult economic circumstances and parlous fiscal condition.”

Gates’s call for “root-and-branch” changes and his questioning of whether the current number of headquarters, flag-officers and commands were necessary could trigger a struggle with groups that have major clout in Congress.

Jacques Gansler, who served as the Pentagon’s chief weapons buyer from 1997 until 2001, said Gates’ biggest hurdle may be winning over members of Congress who are liable to say: “‘We all want to make savings but not in my district.’”

Gansler said the secretary’s goal of saving 3 percent was doable through efficiencies such as greater competition for contracts, streamlining computer systems and easing requirements that half of all maintenance work on U.S. weapons systems be done at U.S. government depots.

“We’ll get this done,” Gates said, promising to spearhead a review to reduce wasteful spending and slash bureaucratic overhead. But it is unclear how long Gates will remain in the job to follow through on what he acknowledged would be a “long-term process.”

Gates already has angered some vested interests by persuading Congress to cut, kill or limit a number of big-ticket military programs, including Lockheed Martin Corp’s premier F-22 fighter. On Monday, he again questioned the need for a projected $13.2 billion landing-craft program for the Marine Corps. The so-called Expeditionary Fighting Vehicle is to be built by General Dynamics Corp.