In an interview with Fox News Sunday, Obama stopped short of saying when - or if - Mubarak would step down, but said he couldn't predict what the next step was.
"Only he knows what he's going to do," he said adding, he couldn't make Mubarak, who has long been an ally of the US, do anything.
"What we can do is we can say the time is now for you to start making change in that country," he said.
"Egypt is not going to go back to what it was," he said. "The Egyptian people want freedom, they want free and fair elections, they want a representative government, they want a responsive government. And so, what we've said is you have to start a transition now..."
Obama said that the US has told Mubarak publicly and privately for many years that he cannot continue to suppress the Egyptian people.
"Part of the message that I think we're seeing all around the world is when you resort to suppression, when you resort to violence, that does not work," he said. Asked if the Muslim Brotherhood is a threat to the US, Obama said the opposition Islamist umbrella group are anti-US, but stressed that is only one faction in Egypt and that they don't have majority support.
"They don't have majority support in Egypt, but they are well organized and there are strains of their ideology that are anti-US." Obama salso said that the future of Egypt is in the hands of its people, and that their options consist of more than the current situation or the Muslim Brotherhood.
"(But) there are a whole bunch of secular folks in Egypt, there are a whole bunch of educators and civil society in Egypt that want to come to the fore as well."
Obama said he's confident Egypt can have an orderly transition process that leads to a representative government "we can work with together as a partner."