Obama was expected to announce the nomination of Clapper, a retired Air Force three-star general, as national intelligence director in a Rose Garden ceremony Saturday.
Two senior administration officials, who spoke only on condition of anonymity ahead of the announcement, confirmed Clapper was Obama's choice.
He would replace retired Adm. Dennis Blair, who resigned last month after frequent clashes with the White House.
The move comes despite objections by some lawmakers in both parties, who complain Clapper had been combative and sometimes obstructive under questioning on Capitol Hill in his previous intelligence roles.
His critics also question whether the former general will have any sway in Obama's influential intelligence inner circle, which includes senior counterterrorism adviser John Brennan and CIA Director Leon Panetta.
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The position of national intelligence director was created in 2004 to coordinate the 16 intelligence agencies in an effort to address the intelligence failures that led to the Sept. 11, 2001, terrorist attacks.
Clapper served as director of the Defense Intelligence Agency, which often works closely with the CIA. In retirement, he became the first civilian director of the National Geospatial-Intelligence Agency, with a few years in private sector focusing on intelligence issues in between.
He has won many fans in the military community and is known for his blunt, sometimes salty speech and direct manner.
But that manner has made for critics on Capitol Hill.
Rep. Pete Hoekstra, R-Mich, said Clapper was the wrong choice, because, he said, he showed disdain for Congress and the oversight process.
Hoekstra and other lawmakers also questioned whether the retired general would fare any better than his predecessor Blair in clashes with the CIA's Panetta
- an administration insider and former lawmaker himself, with a reputation for knowing how to work the system.