The Obama administration said Tuesday that Pakistan was reopening its supply lines into Afghanistan, after the US belatedly issued an apology for the November killing of 24 Pakistani troops in a Nato airstrike.

Secretary of state Hillary Clinton expressed her condolences for the deaths in a telephone conversation with Pakistani foreign minister Hina Rabbani Khar. The incident badly damaged already strained relations between the two countries and forced the US and its allies to send supplies via costlier northern routes into Afghanistan.

"We are sorry for the losses suffered by the Pakistani military," Clinton said in a statement, recounting her discussion with Khar. "I offered our sincere condolences to the families of the Pakistani soldiers who lost their lives. Foreign minister Khar and I acknowledged the mistakes that resulted in the loss of Pakistani military lives."

It is the first time any US official has formally apologised for the deaths, a step hotly debated within the Obama administration and one demanded by Pakistan while its supply routes remained closed for seven months. It came as key Pakistani civilian and military leaders were meeting Tuesday evening in Islamabad to discuss whether to reopen Nato supply routes.

Clinton said a decision had been reached. "I am pleased that foreign minister Khar has informed me that the ground supply lines into Afghanistan are opening," Clinton said. She said Pakistan won't charge any transit fee, the subject of an earlier negotiation, and that the reopening would help the US draw down its war in Afghanistan "at a much lower cost".

"This is a tangible demonstration of Pakistan's support for a secure, peaceful, and prosperous Afghanistan and our shared objectives in the region," she said, calling the agreement "critically important to the men and women who are fighting terrorism and extremism in Afghanistan".

US defence secretary Leon Panetta also welcomed Pakistan's decision. "As I have made clear, we remain committed to improving our partnership with Pakistan and to working closely together as our two nations confront common security challenges in the region," he said.