Pakistani Prime Minister Nawaz Sharif told Pentagon chief Chuck Hagel on Monday that US drone strikes were "counter-productive" as Washington pushed for supply routes to Afghanistan to be kept open.

In the first visit by a US defence secretary for nearly four years, Hagel flew from Kabul to Pakistan to meet the premier and the country's new army chief, General Raheel Sharif.

Ties have been seriously strained over US drone strikes in Pakistan's tribal belt as well as over sanctuaries for Afghan Taliban insurgents inside Pakistan's borders.

Sharif "reaffirmed Pakistan's support for the Afghan peace and reconciliation process", a Pakistan government statement said after the talks.

"The Prime Minister also conveyed Pakistan's deep concern over continuing US drone strikes, stressing that drone strikes were counter-productive to our efforts to combat terrorism."

President Barack Obama has defended the drone strikes as an effective, lawful tool used with restraint to target suspected Al-Qaeda militants.

But human rights groups and Pakistani politicians say the missile attacks have killed innocent civilians and are a beach of sovereignty.

The visit came after Hagel's deputies withdrew a statement that NATO shipments out of Afghanistan through Pakistan would resume due to the end of anti-drone protests.

In recent weeks, activists opposed to the drone raids forcibly searched trucks in northwest Pakistan in a campaign to disrupt NATO supply routes through the Torkham gate border crossing.

The club-wielding protesters have prompted US officials to halt the shipments to protect the truck drivers.

Hagel warned Sharif that US lawmakers could withhold military assistance if Islamabad failed to ensure security for the key supply route.

"There will be those home back in Congress... who will seize upon this issue if it continues to be a concern," a defence official, who spoke on condition of anonymity, told reporters after Hagel's talks with the prime minister.

The US provides major defence aid to Pakistan, including "coalition support funds" in which Washington reimburses Islamabad for the cost of counter-terrorism operations.

"The secretary made the point that we need to demonstrate the continued flow of goods in order to be able to continue fulfilling their reimbursements," the defence official said.

Torkham gate is the main overland route used by the Americans and NATO to withdraw military hardware from Afghanistan as part of the troop pullout set to wrap up by the end of 2014.

Hagel's trip to Pakistan was also to establish a constructive dialogue with Pakistan's new army chief Sharif, who is expected to be at the centre of sensitive security decisions.

"Issues concerning (the) defence relationship, Pak-US bilateral ties and regional stability came under discussion," the Pakistan military said after Hagel met the army chief.

Pakistan is seen as crucial to peace in neighbouring Afghanistan as it was a key backer of the hardline 1996-2001 Taliban regime in Kabul and is believed to shelter some of the movement's leaders.

Pakistan is also battling a homegrown Islamist insurgency, but US officials have long accused Islamabad's spy service of maintaining ties to the Afghan Taliban.

Hagel visited Pakistan after two days in Afghanistan, where he urged President Hamid Karzai to sign a much-delayed pact that will allow some NATO forces to stay in the country after 2014.

Hagel began his trip last week in Bahrain, trying to reassure Gulf allies that the United States would retain a robust military presence in the region despite an interim nuclear deal with Iran.

Hagel left Pakistan on Monday for Saudi Arabia and Qatar, where he was expected to renew his message of solidarity with the Gulf Arab states.

The Saudis in particular are wary of the diplomatic opening with Shiite-led Iran, which they see as a regional rival.