The president spoke a day after Central Intelligence Agency Director Porter Goss complained that the new law would create "ambiguities" between his authority and that of Bush's nominee to be National Intelligence Director John Negroponte, and Defence Secretary Donald Rumsfeld.
"The reforms will help the CIA do its job better," Bush said on Thursday after touring the spy agency.
Bush said he recognised that there were some ambiguities and some CIA employees were uneasy about the changes.
"I know there is some uncertainty," he said, but "I am confident the process will work."
In rare public comments, Goss on Wednesday had said the new law left him unclear on his own future role.
"It's got a huge amount of ambiguity in it," he said. "I don’t know by law what my direct relationship is with John Negroponte, Defence Secretary Donald Rumsfeld or other top officials involved with intelligence," Goss said.
Bush also reiterated that the hunt for Usama bin Ladin goes on even though the al-Qaida chief blamed for the September 11 attacks on the United States has yet to be found.
"We spend everyday trying to find the elusive al-Qaida leader," he said.
Bush also repeated his demand that Syria move all of its forces out of Lebanon as soon as possible. The Syrians have some 15,000 troops in Lebanon.
He said that "the message is loud and clear" from the United States, Europe and Russia that "it is time for Syria to get out".