The officials said Negroponte, who was put at the helm of national intelligence less than two years ago, would play a key role in creating U.S. policies for Iraq in his new position, The New York Times reported Thursday.
The shift is the latest in a string of departures from top intelligence posts since George Tenet resigned as head of the CIA in 2004.
Senior State Department officials said Secretary of State Condoleezza Rice has had difficulty filling the deputy position and has offered it to several other parties who rejected it.
Officials from two federal agencies told the Times the leading candidate for the intelligence chief post is J. Michael McConnell, a retired vice admiral and head of the National Security Agency from 1992 to 1996. He led the Joint Chiefs of Staff during the Persian Gulf War of 1991.