President Barack Obama signed a $633 billion defense bill for next year despite serious concerns about the limits Congress imposed on his handling of terror suspects and lawmakers’ unwillingness to back the cost-saving retirement of aging ships and aircraft. 

Obama had threatened to veto the measure because of a number of concerns, but relented because he couldn’t pick and choose specific sections. However, in a statement, the president spelled out his concerns about restrictions on his ability to carry out his constitutional duties as commander in chief.

Specifically, he complained that the bill limits the military’s authority to transfer third-country nationals being held at a detention facility in Parwan, Afghanistan. He also took issue with restrictions on his authority to transfer terror suspects from the U.S. military prison at Guantanamo Bay, Cuba.

“Decisions regarding the disposition of detainees captured on foreign battlefields have traditionally been based upon the judgment of experienced military commanders and national security professionals without unwarranted interference by members of Congress,” Obama wrote. 

He said the section of the bill related to detainees in Afghanistan “threatens to upend that tradition, and could interfere with my ability as commander in chief to make time-sensitive determinations about the appropriate disposition of detainees in an active area of hostilities.”

Obama promised when he took office four years ago to close the prison at Guantanamo, but congressional opposition from Republicans and some Democrats have prevented him from fulfilling that vow. The law limits his authority to transfer terror suspects to foreign countries or move them to the United States.

Obama insisted that he still believes that Guantanamo should be shuttered because operating the facility “weakens our national security by wasting resources, damaging our relationships with key allies and strengthening our enemies.”

The president said his administration will interpret the bill’s provisions and if they violate the constitutional separation of power, he will implement them in a way to avoid that conflict.

The law puts off the retirement of some ships and aircraft, and Obama warned that the move could force reductions in the overall size of the military as the Defense Department faces cuts in projected spending.  

The law includes cuts in defense spending that the president and congressional Republicans agreed to in August 2011, along with the end of the war in Iraq and the drawdown of American forces in Afghanistan. And it would authorize $528 billion for the Defense Department’s base budget, $17 billion for defense and nuclear programs in the Energy Department and $88.5 billion for the war in Afghanistan.  

The measure is about $29 billion under the current level, largely due to smaller amounts for Iraq and Afghanistan.  

The measure tightens penalties on Iran to thwart its nuclear ambitions and bulk up security at diplomatic missions worldwide after the deadly Sept. 11 raid in Libya.   

As suicides among active-duty soldiers have accelerated, the bill also allows a commander officer or health professional to ask if a member of the services owns a firearm if they consider the individual at risk for either suicide or hurting others.  

The bill includes a Senate-passed provision sponsored by Sen. Jeanne Shaheen, D-N.H., that expands health insurance coverage for military women and their dependents who decide to have abortions in cases of rape and incest. Previously, health coverage applied only to abortions in cases where the life of the mother was endangered.   

The measure includes a 1.7 percent pay raise for military personnel. 

The legislated sanctions would hit Iran’s energy, shipping and shipbuilding sectors as well as Iran’s ports, blacklisting them as “entities of proliferation concern.” The bill would impose penalties on anyone caught supplying precious metals to Iran, and sanctions on Iranian broadcasting.  

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Associated Press writer Donna Cassata in Washington contributed to this report.