CIA chief Porter Goss abruptly resigned today just 13 months after taking up his position.
US President George W Bush thanked him for his "candid advice" during a time of transition.
Neither man explained why Mr Goss was leaving and no replacement was announced. An administration official said Mr Negroponte may recommend a successor as early as Monday.
"He's led ably," Mr Bush said as he sat next to Mr Goss in the Oval Office of the White House.
Mr Goss who was assigned to rebuild the agency after the twin intelligence breakdowns of September 11 and Iraq, quit under pressure connected to recent discussions Mr Bush had been having with national intelligence director John Negroponte.
The CIA lost clout when it fell under a newly-created director of national intelligence as part of reforms following intelligence failures prior to September 11.
Some bureaucratic wrangling resulted as the new intelligence arm sought to assert itself. At his confirmation hearing in September 2004, Mr Goss said he should, like the national intelligence director, have direct access to the President.
Mr Goss said he believed the CIA was "on a very even keel, sailing well."