She envisions a force that "will not tolerate either sectarian actions or any kind of armed assault on the people of Iraq."
Clinton said Iraq had made great strides, despite the latest violence that has killed dozens of people.
The secretary of state arrived in Baghdad a day after back-to-back suicide bombings killed 71 people outside the most important Shiite shrine in Baghdad.
Those attacks came after 88 people were killed by suicide bombers in Baghdad and Muqdadiyah, north of the capital, on Thursday.
Although the violence is at its lowest levels since the months following the 2003 U.S.-led invasion, the latest bombings came amid an increase in high-profile sectarian attacks that raised concerns about the abilities of Iraq's security forces.
They exposed gaps in security as Iraq takes over from U.S. forces in protecting the country. Prime Minister Nouri al-Maliki ordered a military task force to investigate the attacks and how the assailants were allowed to slip through.
The Pentagon plans to hand over responsibility for most urban security in about three months as part of the Obama administration's goal of a complete exit of U.S. forces by the end of 2011.
U.S. officials say they are still committed to the June 30 deadline to move all forces outside major cities, including Baghdad.
But the top U.S. commander in Iraq, General Raymond Odierno, has said American troops could "maintain a presence" in some cities if requested by the Iraqis.
Speaking to reporters ahead of her arrival in Baghdad, Clinton praised Iraq's progress and said that this week's deadly suicide bombings are a sign that extremists are afraid the government there is succeeding.
"I think that these suicide bombings ... are unfortunately, in a tragic way, a signal that the rejectionists fear that Iraq is going in the right direction," Clinton said.
"I think in Iraq there will always be political conflicts, there will always be, as in any society, sides drawn between different factions, but I really believe Iraq as a whole is on the right track," she said, citing "overwhelming evidence" of "really impressive" progress.
"Are there going to be bad days? Yes, there are," Clinton said. "But I don't know of any difficult international situation anywhere in the world or history where there haven't been bad days."
Clinton, who made three trips to Iraq while she was serving in the Senate, was met at the airport by the chairman of the U.S. Joint Chiefs of Staff, Admiral Mike Mullen, who was also on an unannounced trip to Baghdad, and America's new ambassador to Iraq, Christopher Hill, who presented his credentials to the Iraqi government late on Friday.
She attended a closed-door briefing from Mullen and Odierno to discuss the upsurge in violence.
Separately, there is word that Iraq's Cabinet is drafting a law to allow the government to delay payments for its large-scale reconstruction projects.
In a statement issued Friday, the government says plummeting oil prices and limited exports have made it difficult to secure the
cash needed to pay for reconstruction projects.