NATO shipments from Afghanistan via Pakistan are due to resume after the end of anti-drone protests, officials said, as US Defense Secretary Chuck Hagel headed to Islamabad for talks on Monday.

Hagel, who has been in Afghanistan since Saturday, will meet with Prime Minister Nawaz Sharif in the first visit by a Pentagon chief to Pakistan for nearly four years.

Ties between Washington and Islamabad have been deeply troubled over US drone strikes targeting suspected militants in Pakistan's tribal belt, while American officials have long accused Islamabad of allowing Afghan Taliban sanctuaries inside its borders.

In recent weeks, activists opposed to the drones forcibly searched trucks in northwest Pakistan in a campaign to disrupt NATO supply routes to and from Afghanistan.

But a US defence official told reporters in Kabul that the suspension of shipments via Pakistan had been lifted because the protests had stopped, allowing NATO trucks to move safely through the Torkham gate pass.

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

"Secretary Hagel met with Prime Minister Sharif on his visit to Washington earlier this year and looks forward to continuing candid and productive conversations," Pentagon spokesman Carl Woog told reporters on Sunday.

"Secretary Hagel also looks forward to discussing with Prime Minister Sharif and other senior Pakistani officials the United States and Pakistan's common interest in a stable Afghanistan."

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.

Hagel told US troops in Afghanistan on Sunday that he supported a NATO force in Afghanistan after 2014, as wrangling continues between Washington and President Hamid Karzai over a stalled security pact.

Hagel met troops a day after further tensions arose over the Bilateral Security Agreement (BSA), which would allow a small US-led force to stay in the country after most combat troops withdraw.

"I believe there is a role for our coalition partners and the United States, but that depends on the Afghan people," Hagel told soldiers in a question-and-answer session at Camp Bastion in Helmand province.

US commanders were looking at "a new phase for our mission to train, assist, advise and counter-terrorism", he added.

In an interview with CBS television, Hagel later expressed guarded optimism that Karzai, who has a history of stormy relations with Washington, would sign off on the deal in the end.

"I think the more he involves himself, President Karzai, and listens to his people, which leaders must do, I hope he'll come to the right decision on this," he said.

But Hagel acknowledged there was a "very real possibility" that the Americans and NATO would have to completely withdraw, with serious consequences for Afghanistan's stability.

Meetings with Karzai have been customary over the years for Pentagon chiefs, but Hagel did not meet the Afghan president during his visit. The move signalled an apparent shift in tactics, with Washington choosing not to rush to the presidential palace for more urgent talks.

Hagel had said there was no point in him repeating the US position after visits by top American envoys.

Hagel did meet the Afghan defence minister on Saturday, Bismillah Khan Mohammadi, who assured him the security agreement would be signed in "a timely manner".

Karzai has said the signature could take place after the presidential election in April, but Hagel said that would push the timeline into mid-2014 since the polls are expected to result in a run-off vote.

Karzai on Sunday visited neighbouring Iran where President Hassan Rouhani expressed his opposition to the BSA.

Iran "is opposed to the presence of any foreign force in the region, the Middle East, the Persian Gulf and particularly the Islamic country of Afghanistan," Rouhani told Karzai.

There are currently 46,000 US troops and 27,000 soldiers from other coalition countries in Afghanistan, and almost the entire NATO-led force is scheduled to pull out by the end of next year.

Under a proposed post-2014 mission, roughly 12,000 troops -- mostly American -- would remain in the country to train Afghans and counter Al-Qaeda-linked militants.