"I strongly condemn these unjust actions," Obama said in a news conference at the White House.
In Tehran, chaotic images of riot police beating and shooting protesters have seized the world's attention and heightened pressure on Obama to act -- or at least speak out more strongly.
At least 17 people have been killed in protests since the election last week.
Protesters in Iran have demanded that the government there cancel and rerun the elections that ended with a declaration of overwhelming victory for hardline President Mahmoud Ahmadinejad. Reformist presidential candidate Mir Hossein Mousavi says he won and has claimed widespread fraud.
"I have made it clear that the United States respects the sovereignty of the Islamic Republic of Iran, and is not interfering in Iran's affairs," Obama said. "But we must also bear witness to the courage and dignity of the Iranian people, and to a remarkable opening within Iranian society. And we deplore violence against innocent civilians anywhere that it takes place."
Obama noted the killing of a young woman, Neda Agha Soltan, whose apparent shooting death was captured on video and circulated worldwide.
"We have seen courageous women stand up to brutality and threats, and we have experienced the searing image of a woman bleeding to death on the streets," Obama said. "While this loss is raw and painful, we also know this: Those who stand up for justice are always on the right side of history."
Asked if Iran will face consequences for how it has acted, Obama said the world is watching and Iran's handling of dissent "will help shape the tone not only for Iran's future but also its relationship to other countries."
Five months into his presidency, Obama also pushed lawmakers to deliver on ambitious overhauls of health care and energy.
His appearance came as his approval rating -- while still high, and a little above average for new presidents -- was slipping according to recent polls.
The president took the podium after a troublesome week for the new administration. He's seeking to frame the Washington debate on his own terms after a stretch in which he saw fellow Democrats fretting about the jaw-dropping cost estimates of reforming health care, a series of polls underscoring deep unease among independents and moderates over the soaring deficit, and Republicans challenging him to be stronger in his response to the postelection turmoil in Iran.
Obama didn't rule out shifting U.S. strategy on Iran, which now calls for an opening of dialogue.
"We are going to monitor and see how this plays itself out before we make any adjustments about how we proceed," the president said.
Obama said the United States has provided a path for Iran to reach out to the international community and engage with global powers.
"It is up to them to make a decision about whether they choose that path," Obama said. He added that the outlook "obviously is not encouraging in terms of the path that this regime may choose to take."
Obama forcefully countered the idea that he's been slow to forcefully respond to Iran's violent crackdown on dissent. "I don't think that's accurate," Obama said. "Track what I've been saying."
The president said he quickly responded after the election results and after violence broke out in the streets of Tehran, and that the United States has frequently condemned infringements on the freedom of assembly and speech for Iranians.
"We've been entirely consistent," Obama said.
On the home front, Obama is asking Congress to pass a sprawling and costly plan to overhaul the nation's health care system, as powerful interest groups warily react with both support and criticism. On energy, Obama and Congress are under pressure to pass climate and energy legislation by the end of this year, when the U.S. will sit down with other nations to hammer out a new international agreement to curb emissions linked to global warming.
The president used his opening statement to push both measures.
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