House and Senate conferees agreed on $662.4 billion for the fiscal 2012 defense authorization bill, about $26.6 billion below the president’s original request, reflecting the level of reductions in national security spending required under August’s budget agreement.

Almost all the cuts were made in the Pentagon’s core budget, with only $2.3 billion coming out of funds for Afghanistan and Iraq, and $1.2 billion from the nuclear weapons program.

Conferees from the House and Senate Armed Services committees made significant changes to hundreds of budget items, from military aid for Pakistan to the electromagnetic railgun project, an effort to weaponize electromagnetic pulses — something Republican candidate Newt Gingrich referred to in a recent presidential debate.

The conferees froze almost $700 million in aid to Pakistan until the Defense Department provides Congress a report on the strategy and effectiveness of that assistance. The report also must describe Pakistani efforts to implement the U.S. strategy against makeshift bombs, such as limiting the amount of certain fertilizers crossing the border to the Afghan Taliban.

The electromagnetic railgun uses a non-explosive bullet to hit incoming missiles. The Navy has spent more than $200 million for research on the program since 2005, in part because the gun eliminates the need for an explosive charge aboard a ship. Instead, an electromagnetic pulse fires a projectile at almost the speed of sound.

The Senate wanted to eliminate the program, while the House sought to continue funding but mandate a report on the “feasibility” of its development and deployment. Under the agreement, the Navy secretary is required to provide a report on the system within six months.

On the controversial next-generation F-35 Joint Strike Fighter, Congress required the contract for the next 18 aircraft to be at a fixed price and insisted that the manufacturer assume responsibility for cost overruns. About 20 percent of the funds allocated for fiscal 2012 will be held back until the defense secretary can report on the aircraft’s operation and sustainment costs. The conferees also required reports on the Marines’ vertical-takeoff version of the F-35, which has been plagued with problems.

The conferees agreed to make the head of the National Guard Bureau a member of the Joint Chiefs of Staff, despite opposition from the chairman of the Joint Chiefs, Gen. Martin Dempsey. The provision specifies that the leader of the Guard is there with “the specific responsibility of addressing matters involving non-Federalized National Guard forces in support of homeland defense and civil support missions.”

On the fee for Tricare, the military retiree health program, the conferees tied any future increase to the percentage by which retiree pay goes up.

Although there has been little public notice, much of the health care for active and retired military members is now being carried out by contracted medical services. The conferees accepted a House amendment that requires the comptroller general to report by March 31 on the military departments’ contracting of health services for members of the armed forces, their dependents and retirees.

The agreement provides the Joint Improvised Explosive Device Defeat Organization with $2.5 billion for systems to reduce the effectiveness of homemade bombs, which have been a scourge for American troops in Iraq and Afghanistan. While some wanted to eliminate the agency after U.S. combat troops leave Afghanistan, the conferees instead required monthly reports in the coming year on JIEDDO’s obligations and expenditures.

The bill also temporarily halts the building of new Web sites under the Pentagon’s Trans Regional Web Initiative, which has set up foreign-language news sites for North Africa, Central Europe and Iraq. Before any new site can be launched, Defense Secretary Leon E. Panetta must certify what its target audience is, the best and most cost-effective medium to reach those people, and how that audience is to be measured.

A House provision to reduce the costs of Defense Department military bands from $320 million to $200 million was dropped from the final bill.

The conferees trimmed back a number of House provisions that deal with nuclear forces, including one that would have delayed reductions called for under the New Strategic Arms Reduction Treaty with Russia.

The agreement also requires the president to report any changes in the nuclear targeting strategy, modifying House language that would have held up such changes.

The bill is expected to go to a vote in the full House and Senate this week.