Frank Wisner, an influential retired diplomat and former US ambassador to Egypt who met with Mubarak at Obama's request this week, "was speaking for himself and not for the US government," a senior Obama administration official said in Washington.
Wisner called Mubarak an "old friend" of the United States, and said he "must stay in office in order to steer those changes through."
"President Mubarak's continued leadership is critical," Wisner told the Munich Security Conference via video link.
"Frank Wisner was speaking as a private citizen... analyst... not as a representative of the US government," the US official said on condition of anonymity.
Obama meanwhile "discussed his serious concern about the targeting of journalists and human rights groups, and reaffirmed that the government of Egypt has a responsibility to protect the rights of its people and to release immediately those who have been unjustly detained," the White House added.
He also "emphasised the importance of an orderly, peaceful transition, beginning now, to a government that is responsive to the aspirations of the Egyptian people, including credible, inclusive negotiations between the government and the opposition."
The leaders agreed to stay in close contact going forward, the White House said.
The statement came as Washington welcomed as a "positive step" the mass resignation of leaders of Mubarak's party, as it seeks to prod the strongman to the exit. US officials hailed the move but urged more change.
"We view this as a positive step toward the political change that will be necessary, and look forward to additional steps," said the Obama administration official.
Separately, US Vice President Joe Biden told his Egyptian counterpart Saturday that "immediate steps" are needed on democratic reforms.
Biden, in a telephone call to Egyptian Vice President Omar Sulaiman, "asked about progress in beginning credible, inclusive negotiations for Egypt's transition to a democratic government to address the aspirations of the Egyptian people," the White House statement said.
"He stressed the need for a concrete reform agenda, a clear timeline, and immediate steps that demonstrate to the public and the opposition that the Egyptian government is committed to reform."