The House Armed Services Committee reversed several Obama administration national security policies and re-ordered Pentagon weapons spending in its annual defense authorization bill passed early Thursday morning.

After more than 12 hours of debate, the panel backed the fiscal 2012 defense authorization measure (HR 1540) with strong bipartisan support, 60-1. Democrat John Garamendi of California was the lone member to oppose it. The House is expected to consider it later this month.

Overall, the bill would authorize $553 billion for the Defense Department, $18 billion for national security programs at the Energy Department and $118 billion for the wars in Iraq and Afghanistan.

A closely watched vote on the future of the Afghanistan war never materialized at the markup. A growing number of lawmakers have questioned the future of, and even the need for, the U.S.-led mission in Afghanistan in the wake of the Osama bin Laden killing.

Garamendi proposed and then withdrew an amendment that would have barred the administration from having more than 25,000 U.S. troops in Afghanistan by the end of 2012 and would have set the limit at 10,000 troops by the end of 2013. Garamendi said he would offer his proposal on the House floor.

The committee also weighed in on the issue of detainees at Guantánamo Bay, Cuba, by barring the Defense Department from spending any money to transfer or release them into the United States. The provision is widely seen as a rebuff to plans to have those detainees face trials in civilian courts. The panel rejected, 22-38, an amendment offered by ranking Democrat Adam Smith of Washington that would have lifted the ban.

“The United States does not want to be in the business of warehousing low-level terrorists for an undetermined period of time. These are basic principles that this legislation does not recognize,” Smith argued.

The Pentagon’s plan for repealing a ban on openly gay individuals from serving in the military could be delayed or scrapped altogether under the bill.

The panel adopted an amendment that would not allow implementation of a repeal of the ban on gays serving in the military, commonly called “don’t ask, don’t tell,” until all the members of the Joint Chiefs of Staff certify that the change would not be harmful to the military and “will not degrade the readiness, effectiveness, cohesion, and morale of combat arms units.”

Last year, the chiefs of the Army and Marines Corps told lawmakers they had concerns about timing of such a repeal, saying it could disrupt their combat forces in the Middle East.

The amendment, offered by Republican Duncan Hunter of California, was adopted 33-27 in a largely party-line vote. Chris Gibson of New York and Todd Platts of Pennsylvania were the only members of the GOP to oppose the measure, while Mike McIntyre of North Carolina was the only Democrat to support it.

Last year, a lame-duck Congress cleared the legislation that essentially overturned the 1993 law (PL 103-160), marking an achievement for President Obama, who had said during his presidential campaign it was possible to repeal the law.

Under the fiscal 2011 defense authorization law (PL 111-391), certification that the ban would not harm military readiness is required only from the chairman of the Joint Chiefs of Staff, the Defense secretary and the president. Upon introducing the amendment, Hunter argued that the administration should not have the final say on implementing a repeal of the law.

“We give the service chiefs the opportunity to sign off on this and have the Marine Corps say if it’s ready for this,” Hunter said. “What I want is to have the warfighters have a say on this.”

Democrats opposed to the amendment stressed that Congress held a battery of hearings last year with the service chiefs and other officials to ensure the repeal would be manageable.

“Having openly gay Americans serve in the military is not a sign of the apocalypse; it’s a sign of progress,” said Hank Johnson, D-Ga.

The committee expects to complete marking up the defense authorization bill that would authorize $690 billion on Wednesday night or early Thursday morning. The mark thus far defies the administration on several multibillion-dollar programs and policy provisions.

The bill would authorize $118 billion for overseas contingency operations, which are the wars in the Middle East, and $18 billion for national security programs at the Energy Department.

The panel adopted along party lines Wednesday an amendment that would block the president from unilaterally reducing the U.S. nuclear weapons stockpile below levels agreed to in a new treaty with Russia.

The provisions also would block any obligation of funds to implement the 2010 strategic arms reduction treaty, known as New START, until the president moves forward on his promises to modernize U.S. nuclear facilities. The treaty’s ratification was narrowly approved by the Senate late last year.

The amendment — offered by Colorado Republican Doug Lamborn but modeled on a bill (HR 1750) offered by Michael R. Turner, R-Ohio, and a companion measure planned by Arizona Republican Jon Kyl on Wednesday in the Senate — would block the secretaries of Defense and Energy from obligating or spending funds from fiscal 2011 through fiscal 2017 to retire weapons covered under the New START agreement. New START covers nuclear-capable bombers, Trident ballistic missile submarines, launch tubes and Trident D-5 submarine-launched ballistic missiles. It also covers Minuteman III intercontinental ballistic missiles and associated silos.

The restriction would be waived after the secretaries of Defense and Energy submit notice to Congress that they are carrying out the modernization plan agreed to by Obama late last year during the New START debate. The restriction would hold until 90 days after the written certification is provided.

The House panel also adopted amendments that would:

• Require the president to notify Congress before implementing any changes to nuclear strategy and preserve the nuclear triad — bombers, nuclear ballistic missile submarines and land-based intercontinental ballistic missiles;

• Prohibit any international agreements limiting U.S. missile defense capabilities except with specific authorization — by a new treaty or act of Congress;

• Sustain the United States’ extended deterrence for NATO by counseling against unilateral reduction, consolidation or withdrawal of nonstrategic nuclear weapons in Europe, without a request from host nations or the NATO High Level Group.

A proposal backed by the committee that could revive a controversial initiative to build an alternative engine for the F-35 warplane will face opposition on the House floor.

The proposal would allow for building another engine if the current Pratt & Whitney engine failed to meet certain goals and additional funding were needed. It was approved by voice vote.

The engine proposal had been written into the legislation by a House Armed Services subcommittee last week and had been expected to spark a fight at the full committee. But opponents opted not to try to strip it out then, saying they will wait until the bill moves to the House floor.

Republican Mike Coffman of Colorado withdrew an amendment he offered during Wednesday’s markup that would have prohibited funding another engine for the fighter plane, but said he would later offer such a measure on the House floor. Coffman said the bill’s current language is “a loophole” to get the General Electric F136 engine program funded.

Coffman’s proposal could have significant support as the House earlier this year rejected funding for a second engine for the Joint Strike Fighter program, led by fiscal conservatives from both parties.

That engine program is opposed by the Obama administration and the Pentagon formally terminated plans for a second engine that would have been built by General Electric, saying it was unneeded and too costly. The current engine program is estimated to cost $110 billion. GE is continuing to fund the program for fiscal 2012 without government support.

Republican Roscoe G. Bartlett of Maryland said the provision, which was included in the tactical air and land section of the bill, is designed to ensure the best engine is incorporated in the Lockheed Martin fighter jet. He vowed to push colleagues to support it when it reaches the floor.

“Many of us believe it was shortsighted for Congress to have failed to fund the F-35 competitive engine program for the remainder of fiscal year 2011,” Bartlett said. “Yes, our country faces major fiscal challenges. However, to continue to fully fund a $1 trillion F-35 aircraft program and not take the opportunity to maintain competition in the $110 billion engine sub-component of the program, is not in the long-term best interests of F-35 readiness or the taxpayers.”

Before approving the tactical air and land section of the bill, the panel adopted 55-5 an amendment offered by Robert Andrews, D-N.J., that would allow GE to continue work on the program as long as it is self-funded. Andrews also said his amendment would allow the Defense Department to own the alternative engine technology.

The measure would authorize $7.7 billion for development and procurement of 32 F-35s and $3.2 billion for the Mine Resistant Ambush Protected vehicle program.

In other action, the committee approved a provision that would limit money for a program to replace the Marine Corps’ Expeditionary Fighting Vehicle, or EFV, until the Navy provides Congress with a cost analysis for the replacement program.

The vehicle, which is used by Marines to travel swiftly by sea and then drive on land, was terminated by the Defense Department earlier this year over cost concerns. Republican Todd Akin of Missouri has raised concerns that the proposed replacements would not perform as well. In a 2010 report, the Government Accountability Office found the unit price for the EFV program since 2000 had increased by 176.5 percent, to $24.3 million.

The committee approved authorizing $14.9 billion for 10 new warships, including two Virginia-class submarines, one Arleigh Burke-class destroyer, four littoral combat ships, one San Antonio-class amphibious ship, one mobile landing platform ship and one joint high-speed vessel.

Lawmakers also approved authorizing $10.5 billion for the U.S. Special Operations Command, a 7 percent increase over fiscal 2011 enacted levels. They also approved authorizing $261.1 billion for operations and maintenance, including funding for the wars in Iraq and Afghanistan.

The panel included a 1.6 percent across-the-board raise in basic pay for uniformed personnel as requested by the Obama administration.

Before marking up sections of the bill, the committee gave voice vote approval to a separate resolution requesting the administration provide in-depth information related to military action in Libya.

The resolution (H Res 208) sponsored by Republican Tom Cole of Oklahoma, would require the Defense secretary to provide Congress within 14 days of adoption any communication it provided to U.S. lawmakers as of Feb. 15 related to the military action in Libya, including the U.S.-led mission Operation Odyssey Dawn or the NATO-led Operation Unified Protector.