"Through this bill, the United States Congress attempts to circumvent longstanding and proven processes for determining whether or not building and operating a cross-border pipeline serves the national interest," Obama wrote in his message to the Senate.
The president added that because "this act of Congress conflicts with established executive branch procedures and cuts short thorough consideration of issues that could bear on our national interest—including our security, safety, and environment—it has earned my veto."
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The White House had regularly insisted that the veto does not represent an opinion on the merits of the pipeline, but rather an insistence that the State Department evaluation not be circumvented.
Opponents of the pipeline have highlighted the potential for a negative environmental impact, as it may increase carbon pollution and could spill into an aquifer that provides much of the freshwater in the Great Plains agricultural states.
McConnell, who made passing the bill a top priority after Republicans gained control of the chamber in November's elections, has framed the measure as a "jobs bill.'' Even if Obama rejects the bill, "the new Congress won't stop pursuing good ideas,'' McConnell said.
"It's embarrassing when Russia and China are plowing ahead on two massive pipelines and we can't get this one no-brainer of a project off the ground," Boehner wrote in his post-veto release, trumpeting the estimated 42,000 jobs the project could support.
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Keystone supporters in the Senate are at least four votes shy of the two-thirds vote needed to override an Obama veto. They have vowed to attach language approving the pipeline in a spending bill or other legislation later in the year that the president would find difficult to reject.
TransCanada's pipeline would carry 830,000 barrels a day of mostly Canadian oil sands petroleum to Nebraska en route to refineries and ports along the U.S. Gulf. It has been pending for more than six years.
—Reuters contributed to this report.