In a carefully worded statement, National Security Adviser Condoleezza Rice said she agreed with President Bush's decision to file a Supreme Court brief opposing the Michigan plan, which awards bonus points to minorities.
But she also drew a distinction between her views on affirmative action and those of the president.
While he came out forcefully against the use of racial preferences in college admissions, Rice said "it is appropriate to use race as one factor among others in achieving a diverse student body."
She said, however, that "race neutral means are preferable."
Rice, the first African-American to hold her influential post, said she discussed the racial preference issue – which falls outside her usual national security portfolio – with the president before he announced his decision in the Michigan case.
Other administration officials have stressed the filing was carefully worded to cover just the Michigan plan, not the high court's landmark Bakke decision. That 1978 ruling outlawed strict quotas, but said admissions officers could take race into account.
White House officials said Rice unsuccessfully urged Mr. Bush to concede that race could be used as a factor in admissions, though she agreed with his view that the Michigan program went too far.
They said Rice was stung by a Washington Post story that said she helped convince the president that favoring minorities was not an effective way of improving diversity on college campuses.
Rice discussed the article with Mr. Bush, who urged her to go public with her differences, officials said on condition of anonymity.
In an interview with the American Urban Radio Network, Rice said she agreed that affirmative action is needed "if it does not lead to quotas."
With a quick defense of her views, Rice is certain to fuel speculation that she harbors political ambitions. Many Republicans consider her a potential presidential or vice presidential candidate.
"My own personal view is that there are circumstances in which it is necessary to use race as a factor among many factors in diversifying a college class," she told the network "And so I've been a supporter of affirmative action that is not quota based and that does not seek to make race the only factor, but that considers race as one of many factors."
White House spokesman Ari Fleischer said, "Dr. Rice has a long record on this issue and she didn't want any media coverage of her position to fail to mention her record. The president welcomes and continues to welcome her helpful input and thoughts."
Making a decision loaded with political implications, Mr. Bush set aside arguments by conservatives who wanted him to argue that race should never be used as a factor. His political advisers feared such an approach would alienate swing voters and minorities who want the GOP to be more tolerant.
Rice's decision to go public with her differing views could be part of a White House effort to show that Mr. Bush is open to a wide range of opinions from a diverse set of advisers, said a GOP strategist close to the president.
At the same time, the president sought to appease conservatives by weighing in against the affirmative action programs instead of exercising his option not to take part in the case.