Ties between Pakistan and the US are improving after hitting a low point, Pakistani Foreign Minister Hina Rabbani Khar insisted Friday, even as violent anti-US protests rocked her country.

Meeting at the State Department, US Secretary of State Hillary Clinton and her Pakistani counterpart vowed to work to put their uneasy alliance back on track after a series of crises between the uneasy allies.

"We have been through some of the most difficult times in our 60-year history," Khar said, admitting "the last 18 months were very, very difficult."

But she said amid concerted efforts the two nations were doing "better than we could have expected to do in building the trust."

"We still have work to do to get our bilateral relationship to the point where we would like it to be," Clinton acknowledged. "But we both recognize that we can achieve more when we work together on a focused agenda."

The two women were meeting against the backdrop of another day of violent protests across Pakistan, targeting American diplomatic missions, and fueled by anger at an anti-Islam film which Muslims say insults their faith.

Witnesses estimated that nationwide rallies mobilized more than 45,000, mainly members of right-wing religious parties and supporters of banned terror groups, although the numbers were still small in a country of 180 million.

As Pakistani police fought back with gunshots and tear gas in five major cities, 20 people were killed and more than 200 wounded.

The State Department has paid $70,000 for ads on Pakistani networks to condemn the film and stress that it had nothing to do with the US government. But the message is failing to get across.

"Today we've once again seen protests in several cities in Pakistan," Clinton said. "Unfortunately, some of those protests have turned violent and, sadly, resulted in loss of life."

But she thanked the Pakistani government for efforts to protect the main US embassy in Islamabad and consulates in Lahore, Peshawar and Karachi, since the protests flared last week.

Clinton again stressed that despite provocation "there is no justification for violence" but Khar made no mention of the protests in her country and did not call on her countrymen to end the demonstrations.

Instead she thanked the US administration for condemning the film, saying: "I think that is an important message, and that message should go a long way in ending the violence on many streets in the world."

Anger in Pakistan has spiked since the killing of Al-Qaeda leader Osama bin Laden in a secret US commando raid on his Pakistani compound in May 2011, and a US airstrike in November which killed more than 24 Pakistani troops.

The incidents saw relations plunge. Islamabad closed border crossings into Afghanistan to NATO convoys, forcing them to take longer, more expensive routes to supply their troops, until the blockade was lifted in July.

But Khar insisted that after efforts to renew the relationship over the past few months "we stand at a time of opportunity."

Earlier in the day, Khar obliquely confirmed there were plans for a secret trilateral talks with Pakistan, Afghanistan and the United States to work on combating terror groups in the region.

"I feel in some ways we are at a turning point," she told the Council on Foreign Relations think tank, when asked about the talks by former US secretary of state Madeleine Albright, adding the idea was already "a work in progress."

"I think it is important that we are able to put our energies together and move to see what we can achieve together in Afghanistan.

"We feel that with ties with the US on a positive trajectory, that we have built enough confidence to start those serious discussions."

Islamabad was very concerned the withdrawal of US and NATO combat troops in 2014 would leave a security vacuum in Afghanistan with which it shares a long and porous border, she said.

Clinton will meet Pakistan's President Asif Ali Zardari next week on the sidelines of the UN General Assembly.