US Vice President Dick Cheney said his chief of staff Lewis "Scooter" Libby would fight the charges of obstruction of justice and perjury brought against him. Mr Libby predicted that an investigation will find him "completely and totally exonerated."
Libby resigned his White House post and faces up to 30 years in prison in a case that has put a spotlight on how the administration sold the nation on the war in Iraq and countered its critics.
President George W. Bush's top political adviser, Karl Rove, was not indicted along with Mr Libby, but special counsel Patrick Fitzgerald has made clear to Mr Rove he remains under investigation and in legal jeopardy, lawyers said.
"It's not over," Fitzgerald told a news conference. Bush said the investigation and legal proceedings were "serious and now the process moves into a new phase."
Reggie Walton, the federal judge chosen to handle Libby's case, was appointed by Bush to the court. An arraignment for Mr Libby to enter a plea has yet to be scheduled.
Despite initial denials, both Mr Rove and Mr Libby spoke to reporters in June and July 2003 about the CIA operative, Valerie Plame.
Mr Libby, who played a major behind-the-scenes role in building the case for the Iraq war, was accused in the five-count indictment of making false statements about how and when he learned and disclosed to reporters classified information about Ms Plame.
Ms Plame's cover was blown after her diplomat husband, Joseph Wilson, accused the Bush administration of twisting pre-war intelligence to support military action against Iraq. Wilson said it was done deliberately to erode his credibility.
"Today is a sad day for America," Mr Wilson said in a statement. "When an indictment is delivered at the front door of the White House, the Office of the President is defiled."
Some Republicans have accused Mr Fitzgerald of being overzealous by pursuing "legal technicalities" instead of the underlying crime. Libby was not charged with illegally disclosing the name of a covert CIA operative.
"I'll be blunt," Mr Fitzgerald said in response. "That talking point won't fly."
He also sought to distance the charges from the growing national debate over the Iraq war, saying the issue was whether "Libby lied or not" and not whether "the war was justified or unjustified."
The charges accuse Mr Libby of lying to FBI agents who interviewed him on October 14th, 2003, and November 26th, 2003, committing perjury while testifying under oath to the grand jury twice in March 2004, and engaging in obstruction of justice by impeding the grand jury's investigation.
Mr Wilson based his criticism of the administration in part on a CIA-sponsored mission he made to Africa in 2002 to check out an intelligence report that Iraq sought uranium from Niger.
Mr Bush cited intelligence that Iraq sought uranium from Africa in his 2003 State of the Union address, but Wilson later said the claim was unsubstantiated.
Mr Cheney's office sought to discredit Mr Wilson and his findings by suggesting the trip had been arranged by his wife.
The indictment showed that Libby began seeking information about Wilson and his wife in late May 2003, some six weeks before Ms Plame's identity was publicly disclosed in a July 14th, 2003, newspaper column by Robert Novak.