"All in all this was a pretty shameful day for Washington," Obama said at a Washington, D.C., news conference after the vote, which was a jarring blow to the drive to curb firearms.
Obama said he considered the loss "just Round 1." He called on Americans who support the expanded background checks to be as politically active and persistent as those who opposed them.
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Obama was flanked by gun violence victims, including former U.S. representative Gabrielle Giffords. He slammed critics who said it was unseemly for the victims to be lobbying for the new law.
"Are they serious? Do we really think that thousands of families whose lives have been shattered by gun violence don't have a right to weigh in on this issue?"
The background check measure commanded a majority of senators, 54-46, but that was well short of the 60 votes needed to advance. Forty-one Republicans and five Democrats sided to scuttle the plan.
The legislation was sparked by December's massacre of children and staff at an elementary school in Connecticut. Obama made broadened background checks the centrepiece of his gun control proposals.
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The roll call was also a victory for the National Rifle Association, which opposed the plan as an ineffective infringement on gun rights. Obama said the gun lobby and its allies "willfully lied" about the bill rather than support a compromise.
The proposal would have required background checks for all transactions at gun shows and online. Currently they must occur for sales handled by licensed gun dealers.
The system is designed to keep criminals and people with mental problems from getting guns.