The probe was opened after Mr Bush earlier in December urged a "full investigation" into the source of leaked information that he had authorised the National Security Agency (NSA) to monitor massive volumes of telephone and Internet communications.
But the White House said on Friday it had no role in the decision to investigate the leak.
"The Justice Department undertook this action on its own, which is the way it should be," White House spokesman Trent Duffy told reporters in Crawford, Texas, where Mr Bush was on vacation at his ranch.
Rights groups, however, quickly branded the investigation a crackdown on critics of the president.
"President Bush broke the law and lied to the American people when he unilaterally authorised secret wiretaps of US citizens," said Anthony Romero, executive director of the American Civil Liberties Union.
"Our nation is strengthened, not weakened, by those whistleblowers who are courageous enough to speak out on violations of the law," Mr Romero said.
Domestic spying is a sensitive issue for many Americans who are proud of their civil liberties. Similar revelations about domestic spying led to legislation in the 1970s that allows wiretapping but requires government agencies to obtain a special court warrant for it.
While the source of the leak remains unknown, media reports have suggested that some agents were concerned about the program's legality.
But Mr Bush and his aides have stressed that the eavesdropping order was limited to those suspected of ties to al-Qaeda, as part of the administration's "war on terror".
Mr Bush's secret 2002 order enabled the NSA to monitor, without a warrant, international telephone calls and electronic mail of US citizens suspected of al-Qaeda links.
The New York Times has reported that the NSA's "data-mining operation" -- often in cooperation with major telecommunications firms – includes surveillance of phone calls outside the US that pass through US-based telephone gateways.
Critics charge that the programs are an abuse of presidential power and violate the 1978 Foreign Intelligence Surveillance Act, which requires a warrant for domestic wiretaps and electronic surveillance.
The Bush administration contends that the program is legal under the US Constitution and a congressional resolution, following the September 11, 2001 terrorist attacks that authorised the use of force in Afghanistan.
Prior to the exposure of the NSA program, though, President Bush repeatedly argued that the controversial Patriot Act package of anti-terrorism laws safeguards civil liberties because authorities still need a warrant to tap telephones in the United States.
"Any time you hear the United States government talking about wiretap, it requires ... a court order," he said in April 2004.
In the wake of the leak, the White House also said that reporting the NSA program in the media helps the country's enemies.
"The leaking of classified information is a serious issue," Mr Duffy said.
Al-Qaeda's playbook is not printed on page one (of a newspaper), and when America's is, it has serious ramifications,” he said.