Rice would not comment on the reported deaths of 18 villagers in a raid said to target Osama bin Laden's deputy. She merely said: "We'll continue to work with the Pakistanis and we'll try to address their concerns."
But speaking to reporters on her way to Liberia for the inauguration of president-elect Ellen Johnson Sirleaf, Rice made no apologies for US actions against suspected al-Qaida forces near the border with Afghanistan.
"It's obviously difficult at this time for the Pakistani government," she said of the attack that sent thousands of Pakistanis into the streets in at least five cities, and prompted an official protest from Islamabad.
"But I think I would just say, to both the Pakistani government and the Pakistani people, we're allies in the war on terror," Rice said, adding al-Qaida and its Taliban allies "are not people who can be dealt with lightly."
"But I think I would just say, to both the Pakistani government and the Pakistani people, we're allies in the war on terror"
the US Secretary of State
"The biggest threat to Pakistan, of course, is what Al-Qaeda has done in trying to radicalise the country, the extremist elements that really occupy ... parts of the country in important ways, (and) tried twice to assassinate President (Pervez) Musharraf."
Asked about Friday's strike reportedly carried out by a missile-firing US Predator drone in hopes of killing al-Qaida's second in command Ayman al-Zawahiri, Rice said, "I can't speak about the specifics of this particular circumstance."
But she said, "The frontier area is extremely difficult and it's been lawless there for a long time. Pakistani forces are operating there, trying to take control. We're trying to help."