Defense Secretary Leon Panetta warned Pakistan on Thursday that Washington is losing patience over its failure to eliminate safe havens for insurgents who attack US troops in neighbouring Afghanistan.

Panetta lashed out at Pakistan and the Al-Qaeda-linked Haqqani network during a brief visit to Kabul overshadowed by fury over a NATO air strike that allegedly killed 18 civilians, an issue that the Pentagon chief did not address in public.

Panetta left Kabul less than five hours after his arrival, as Afghan President Hamid Karzai pledged to cut short a trip to Beijing and head home over the deaths of around 40 civilians Wednesday in the air strike and a suicide bombing.

"Even though we are seeing an uptick in violence in recent days, the overall level of violence is down from past years," said Panetta, who is assessing plans to withdraw US combat troops by the end of 2014.

The Haqqani group, a faction linked to the Taliban and Al-Qaeda that is believed to be based in Pakistan's lawless tribal district of North Waziristan, is blamed for some of the deadliest attacks in Afghanistan's 10-year war.

"It's an increasing concern that this safe haven exists and that there are those like the Haqqanis who are making use of that to attack our forces," Panetta told a news conference with his Afghan counterpart, Abdul Rahim Wardak.

"We are reaching the limits of our patience here," he said.

"For that reason, it's extremely important that Pakistan take action to prevent this kind of safe haven," he said.

"We have made that very clear time and time again and we will continue to do that. But as I said, we are reaching the limits of our patience," he added.

The Afghan and US governments have suggested the war in Afghanistan cannot be won unless safe havens in Pakistan are dismantled.

Analysts say Islamabad allows the Haqqanis to operate to hedge against any influence by their arch-foe India in Afghanistan, while critics in Pakistan accuse the Americans of deflecting blame for the increasingly deadly war.

The Pentagon chief said the Haqqani network was to blame for an attack last week on Forward Operating Base Salerno in eastern Afghanistan.

US military chief General Martin Dempsey, asked about Panetta's remarks, said the strong words on Pakistan were largely because the Haqqani network was more active in eastern Afghanistan, where the transition from NATO forces is expected to be particularly difficult.

Dempsey, chairman of the Joint Chiefs of Staff, told reporters in Washington that he shared Panetta's frustration but acknowledged that Pakistani forces were fighting militants on parts of their own soil.

"Make no mistake about it: Although we are extraordinarily dissatisfied with the effect that Pakistan has had on the Haqqanis, we are also mindful that they are conducting military operations -- at great loss, by the way," he said.

The United States leads 130,000 NATO troops fighting the Taliban insurgency and is planning to withdraw the bulk of combat forces from Afghanistan by the end of 2014, and hand responsibility for security to the Afghans.

But civilian casualties caused by US and NATO air strikes have been a frequent source of tension between Karzai and the United States.

The Afghan president, who was attending a meeting of the Shanghai Cooperation Organisation in Beijing, issued a stinging rebuke of NATO's latest air strike.

"Attacks by NATO that cause life and property losses to civilians under no circumstances could be justified and are not acceptable," Karzai said of the incident on Wednesday in Logar province, south of Kabul.

Karzai "will shorten his trip to China and will very soon return to the country" following the deaths in Logar and those from a Kandahar suicide bombing on the same day, his office said.

NATO's US-led International Security Assistance Force (ISAF) said "multiple insurgents" were killed in the air strike, which was ordered after troops came under fire during an operation against a Taliban commander.

Local police said that 18 civilians, including women and children, were killed in the strike. Dempsey promised an investigation.

The air strike did not come up in Thursday's talks between Panetta and Wardak, a senior US defence official told AFP.

For the past five years the number of civilians killed in the war has risen steadily, reaching a record of 3,021 in 2011, with the vast majority caused by insurgents, the United Nations says.

In Kandahar on Wednesday, 23 civilians were killed when two Taliban bombers blew themselves up at a makeshift bazaar and truck stop near a major NATO base.

Panetta's stop in Kabul came at the end of a nine-day tour with stops in Singapore, Vietnam and India, in which he touted a US strategic shift toward Asia after a decade of war.