President Obama signed into a law a $680 billion defense spending bill on Wednesday that includes a controversial measure extending hate-crime protection to gays.

Obama, who signed the National Defense Authorization Act for Fiscal Year 2010 in an elaborate East Room ceremony at the White House, said the bill finally cuts wasteful weapons projects that some lawmakers have spent years trying to kill. Among them is the Cold War-era F-22 fighter that critics have said is poorly suited for the battles in Iraq and Afghanistan.

The bill also includes a program Obama had threatened to veto, the development of an alternative engine for the F-35 Joint Strike Fighter. The administration said the spending on plans for the second engine was unnecessary and would disrupt the F-35 program.

And the legislation includes a measure -- the Matthew Shepard and James Byrd, Jr. Hate Crimes Prevention Act-- that authorizes the Justice Department to investigate and prosecute violent attacks in which the perpetrator has targeted a victim because of the his or her actual or perceived race, color, religion, national origin, gender, sexual orientation, gender identity or disability.

The measure is named after Matthew Shepard, a gay college student who was brutally murdered 11 years ago in a bias-motivated attack in Wyoming.

"This law honors our lesbian, gay, bisexual and transgender brothers and sisters whose lives were cut short because of hate," Human Rights Campaign president Joe Solmonese said in a statement released Wednesday.  "Today's signing of the first major piece of civil rights legislation to protect LGBT Americans represents a historic milestone in the inevitable march towards equality."

But the bill has come under fire by conservatives because of language they say targets clergy and others who oppose homosexuality on religious grounds and who might express those beliefs publicly.

In a statement released Wednesday, Rep. Mike Pence, R-Indiana, blasted Obama for implementing a "radical" agenda" and putting his "liberal social priorities ahead of an unambiguous affirmation of our men and women in uniform."

"Every day, our Armed Forces stand in defense of freedom and our cherished way of life. It is deeply offensive to their service and to millions of Americans to pile so-called 'hate crimes' legislation onto a bill that authorizes critical resources for our troops. Hate crimes legislation is antithetical to the First Amendment, unnecessary and will have a chilling effect on religious freedom," he said.