"This is a serious investigation," Mr. Bush said at the end of a meeting with his Cabinet. "I will be more than happy to comment on this matter once this investigation is complete.
"I also will not prejudge the investigation based on media reports," he said, when asked whether Rove acted improperly in discussing CIA officer Valerie Plame with a reporter.
Rove talked about Plame – without using her name – in a July 11, 2003, conversation with Time magazine reporter Matthew Cooper. Cooper later wrote an article that identified her.
As CBS News Chief White House Correspondent John Roberts reports, Rove's immediate problem is not likely criminal, but political. President Bush vowed last year to fire anyone found to have leaked classified information. Rove's attorney Robert Luskin insists his client never intended to disclose the identity of a CIA operative, only warn Cooper of potentially bad information. So Mr. Bush must weigh whether that rises to a firing offense.
The president's statement Wednesday was a surprise for some White House advisers and senior Republicans who had expected him to deliver a vote of confidence for Rove, his deputy chief of staff.
Mr. Bush refused to directly answer questions about whether he had spoken to Rove about his discussion with Cooper.
"I have instructed every member of my staff to fully cooperate in this investigation," he said. Rove sat stoically behind Mr. Bush during the questions about his involvement.
White House press secretary Scott McClellan said later that the president didn't express his confidence in Rove because he wasn't directly asked if he supports him. But he said Mr. Bush still has confidence in Rove.
"Every person who works here at the White House, including Karl Rove, has the confidence of the president," McClellan said.
According to Luskin, Rove is in no danger of criminal charges, reports Roberts. Luskin told Roberts that prosecutor Patrick Fitzgerald assured Rove that he is not a target of the investigation. Whether the disclosure of the e-mail exchange with Cooper changes this remains to be seen, but Luskin insists that there is nothing in the e-mail that Rove has not already discussed with prosecutors and the grand jury.
Read of the Rove controversy
Meantime, Cooper was in U.S. District Court on Wednesday to testify before the grand jury investigating the leak. His appearance lasted 2 1/2 hours.
"I testified openly and honestly," Cooper said outside the courthouse, without divulging details of what transpired there. "I have no idea whether a crime was committed or not. That's something the special counsel's going to have to determine," he said.
Cooper had refused to reveal his source for the story but agreed to do so after a confidentiality agreement was waived by Rove. That came just before Cooper could have been sent to jail for not cooperating with the investigation into who in the Bush administration leaked her name and whether that constituted a crime.
Another reporter, Judith Miller of The New York Times, is in prison after refusing to disclose her source to investigators.
Cooper implored special counsel Patrick Fitzgerald to wrap up the case soon so the grand jury can be dismissed. When that happens, Miller will be freed.
In September and October 2003, McClellan said he had spoken to Rove about the Plame matter and that Rove wasn't involved in the leak. McClellan refused for a third day Wednesday to discuss the denials of two years ago, saying that to do so would impinge on the ongoing criminal investigation of the leak.