The chairman of the US joint chiefs of staff arrived in Islamabad on Wednesday for talks with Pakistan's top general expected to address concerns over official links with militants in the region.

Pakistan's Inter-Services Intelligence Agency (ISI) has long-been held to keep contact with militants operating in the wild tribal areas along the Pakistan-Afghanistan border who plague US-led forces fighting the Afghan war.

Admiral Mike Mullen's trip follows a visit to Afghanistan a day earlier in which he told reporters he would raise ongoing concerns with Pakistan Army chief general Ashfaq Kayani, according to the Joint chiefs of staff website.

Mullen praised cooperation between US and Pakistani troops in working jointly to combat the militant Haqqani network who target Nato forces in the Afghan East, but acknowledged "strain" caused by the insurgents' ties with ISI.

"Haqqani is having a much more difficult time now," Mullen told reporters, according to an article on the website.

"All that said, we're still working through the (Pakistani) military support, the way through the relationships the (Pakistani intelligence agency) has with the Haqqani network, and the strain that creates."

The Haqqani network is an Al Qaeda-allied outfit run by Afghan warlord Sirajuddin Haqqani and based in Pakistan's North Waziristan tribal district.

The group has been blamed for some of the deadliest anti-US attacks in Afghanistan, including a suicide attack at a US base in Khost in 2009 that killed seven CIA operatives.

The commander of coalition forces for the Eastern region of Afghanistan, major general John Campbell, told reporters during Mullen's visit that efforts to work with Pakistan to counter the Haqqani threat had improved.

There were complementary operations either side of the border, but he acknowledged: "I don't know at what level they are tied in to the ISI."

Mullen's trip is the latest shuttle diplomacy mission after a fatal shooting by a CIA contractor in January enflamed a row between the US and Pakistan over intelligence sharing and raised tensions over the controversial US drone war.

Pakistan is a key US ally in the war in Afghanistan, and receives billions of dollars in military and civilian aid from the global superpower.

But covert missile strikes targeting militants in Pakistan's lawless border regions, believed to operate with the tacit consent of Islamabad, stoke rampant anti-American sentiment throughout the South Asian nation.

Pakistan has publicly insisted the drones stop and that the US slashes the number of CIA agents on its soil, while US officials say operations will continue in order to prevent more attacks by Al Qaeda-linked militants on the United States.

Pakistan's foreign secretary Salman Bashir left for the United States on Tuesday for two-day talks with state department officials aimed at "bringing back on track" bilateral dialogue, a senior government official told AFP.

During Mullen's on Tuesday visit to forward operating base salerno in Afghanistan, he also acknowledged that the Taliban had grown over the course of the nearly ten-year war and that the upcoming fighting season would be tough.

"We're going to have a very tough year this year," he told reporters.

"I've been very straight with the American people on that. I think our losses, which were significant last year, will be significant this year as well."

In 2010, 499 US troops lost their lives, according to the independent iCasualties.Org website, in the highest annual toll since the war began in late 2001.

Combat troops are set to drawdown in 2014, handing control of nationwide security to Afghan Army and police.