He also said Negroponte's role would be to "lead a unified community" and that the CIA director would report to him.
Negroponte, a surprise choice who had been ambassador to Baghdad for less than a year, met Bush at the White House this week.
The newly created intelligence chief position will oversee 15 US intelligence agencies and emerged as a central recommendation of the commission that investigated the September 11, 2001, attacks last year.
The new intelligence chief also will give Bush his daily intelligence briefing and must be confirmed by the Senate.
The new intelligence director could face struggles similar to those confronted by the Department of Homeland Security, which was also created in response to the September 11 attacks and had a difficult time combining a number of government agencies.