Washington - Pakistan and the United States reached a deal on Tuesday to re-open land routes that Nato uses to supply troops in Afghanistan, ending a seven-month crisis that damaged ties between the two countries and complicated the US-led Afghan war effort.

US Secretary of State Hillary Clinton, in a telephone call with Pakistani Foreign Minister Hina Rabbani Khar, apologised for a November Nato air strike which killed 24 Pakistani soldiers last November and prompted an infuriated Islamabad to slam the supply routes closed.

“We are sorry for the losses suffered by the Pakistani military. We are committed to working closely with Pakistan and Afghanistan to prevent this from ever happening again,” Clinton said in a statement following the conversation.

Khar, in turn, informed Clinton that Pakistan would reopen the supply routes and, in a major concession to the United States, would not follow through on threats to dramatically hike the transit fees.

The deal, which came after several previous attempts at negotiation had failed, opened the prospect of broader improvement in US-Pakistan ties.

But even with this hurdle down, others remain - including Pakistan's opposition to US drone strikes on its territory, and Washington's allegations that Islamabad condones, or even assists, anti-American militants.

In her statement, Clinton said the supply lines agreement “is a tangible demonstration of Pakistan's support for a secure, peaceful, and prosperous Afghanistan and our shared objectives in the region”. She added that the deal would allow the United States and its Nato partners to conduct their planned military drawdown from Afghanistan at a much lower cost.

US officials said the United States was spending $100-million more a month to send supplies across the lengthy alternate route into Afghanistan overland across Central Asia.

The Pakistani Taliban militant group immediately threatened to attack trucks that resume carrying supplies into Afghanistan, where most of the 128 000 Nato soldiers are due to withdraw by the end of 2014.

“We will attack Nato supplies all over Pakistan. We will not allow anyone to use Pakistani soil to transport supplies that will be used against the Afghan people,” the group's spokesperson told Reuters by telephone from an undisclosed location.

US Defence Secretary Leon Panetta, who last month said Washington was losing patience with Pakistan because of the safe havens it offers to insurgents in neighbouring Afghanistan, welcomed the news that the supply routes would re-open.

In an interview with Reuters last month, Panetta had all but ruled out an apology to Pakistan over the Nato airstrike.

Pakistan's Prime Minister Raja Pervez Ashraf told senior government leaders on Tuesday that continued closure of the routes was harming Islamabad's relationship with Washington, and Pakistan's Ambassador to the United States Sherry Rehman said the supply route deal could help to spur more cooperation between the two uneasy partners.

“We appreciate Secretary Clinton's statement, and hope that bilateral ties can move to a better place from here. I am confident that both countries can agree on many critical issues, especially on bringing peace to the region,” Rehman said in a statement.

US-Pakistan ties turned markedly worse after the US raid that killed al-Qaeda leader Osama bin Laden on Pakistani territory last year, and have been further poisoned by the US drone strikes to target suspected militants and Washington's charge that Islamabad turns a blind eye to Haqqani network militants operating from within its borders.

Clinton's careful statement was not the full-throated apology that Pakistan demanded for the deadly November attack, but went further than Washington had before in expressing regret for an incident which Nato described as an unfortunate accident.

“Foreign Minister Khar and I acknowledged the mistakes that resulted in the loss of Pakistani military lives,” Clinton said, adding that she had reiterated US regrets for the deaths of the soldiers and offered condolences to their families.

The US administration, seeking to shield President Barack Obama from Republican criticism months before the US presidential election, had resisted an outright apology and political analysts said the moderate expression of regret came following an expensive delay.

“Three little words - ‘We are sorry’. If they'd been delivered seven months ago, they might have saved hundreds of millions of dollars,” said Jonah Blank, a former aide to US Senator John Kerry who is now at the Rand Corporation.

With a deal reached, both sides were set to benefit.

The agreement appeared to include a commitment by the United States to initially pay Pakistan $1.8-billion in military aid arrears.

But Washington would only have to provide $250 in handling fees for each shipment of Nato supplies going into Afghanistan, the same amount paid on those shipment prior to November. In recent months, Pakistani officials had demanded fee hikes that some suggested could have marked a twenty-fold increase, to about $5 000 per shipment.

Payment of aid arrears could be a windfall for Pakistan's unpopular government, under pressure to deal with a struggling economy, chronic power cuts and inflation in the lead-up to parliamentary elections expected early next year.

Pakistan political analyst Hasan Askari Rizvi said the deal would allow Islamabad to play a greater role as the Nato drawdown gets under way, but also showed up some of the inherent weaknesses in Pakistan's brittle political structure.

“Pakistan's system is so unwieldy that one doesn't know who is making the decisions and who you have to discuss things with. This is a very poor example of crisis management by the Pakistan foreign office and the military,” he said. - Reuters