President George W Bush said he is "troubled" by the justice department's misleading explanations to Congress of why it fired eight US prosecutors.
Mr Gonzales denied knowing specific details about the firings
"Mistakes were made. And I'm frankly not happy about them," Mr Bush said in Mexico, at the end of a week-long trip to Latin America.
Mr Bush said, however, that he stood by Attorney General Alberto Gonzales who is facing calls to resign.
Mr Gonzales has accepted responsibility but denied personal involvement.
Congress has been investigating whether the firing of the eight prosecutors - nearly one in 10 nationwide - was politically motivated. Some have called it a purge.
Mr Gonzales's top aide resigned on Monday as the scandal gathered steam.
"Any time anybody goes up to Capitol Hill, they've got to make sure they fully understand the facts and how they characterise the issue to members of Congress," Mr Bush told reporters.
"And the fact that both Republicans and Democrats feel like that there was not straightforward communication troubles me and it troubles the attorney general. So he took action, and he needs to continue to take action."
Mr Gonzales said on Tuesday that two years ago the White House had proposed dismissing all 93 US attorneys.
That appeared to confirm a report in the Washington Post newspaper that Mr Bush's former counsel, Harriet Miers, had suggested the idea to the justice department.
Serve at the discretion of the president, with the advice and consent of the Senate
Prosecute criminal cases brought by the government
Prosecute or defend civil cases in which the government is a party
Collect debts owed to the government
Source: US Department of Justice
Critics - including some of the former prosecutors themselves - say they were fired for political reasons or to make way for cronies of the administration.
Mr Gonzales said he was aware in general terms of what was happening but never saw documents or participated in discussions about the firings.
In Mexico, Mr Bush said he had never given the attorney general specific instructions and denied as "just not true" allegations about political decision-making.
Judiciary committees in both chambers of Congress are expected to deepen their inquiries into the dismissals of the prosecutors.