"Pakistan's continued acceptance of sanctuaries for Afghan-focused insurgents and failure to interdict IED materials and components continue to undermine the security of Afghanistan and pose an enduring threat to US, Coalition, and Afghan forces," said the bi-annual report on Progress Towards Security and Stability in Afghanistan.
In an interaction with Pentagon reporters, a senior Defence Department official, however, said there has been considerable improvement in relationship with Pakistan.
"In the last couple of months, our relations with Pakistan have improved. There's now a positive trend in the relations between Afghanistan and Pakistan," the official said.
He observed that Pakistani leaders, both civilian and military, have said that they now see a stable and secure Afghanistan as the primary security interest of Pakistan.
"While we, in the report, describe what we see on the ground, I would say what we've heard from the Pakistan (people) over the last several months is very promising," the Defense Department official said.
Meanwhile, another State Department official has said the US is very encouraged by the dialogue process that is taking place between Afghanistan and Pakistan.
"An important and essential part of that dialogue is the cross border situation. So we hope that dialogue will continue. We hope and expect to see confidence building measures from both the Afghans, and the Pakistanis. To the extent that we can be helpful, we want to encourage that dialogue in the interest of peace and stability.
"The US continues to seek a relationship with Pakistan that is constructive and, advances both US and Pakistani interests," the report said, noting that while Islamabad has contributed to Washington's interests, it has simultaneously fallen short in other areas.
"Pakistan has publicly declared its support for an Afghan-led reconciliation process and continues to cooperate on some counter-terrorism activities, bolstering US efforts to disrupt and defeat Al Qaeda," it said.
Pakistani military operations against Tehrik-e-Taliban (TTP) and other militant groups in the Federally Administered Tribal Areas (FATA) and Khyber Pakhtunkhwa since 2009 have significantly disrupted insurgent groups in Pakistan, while also resulting in significant military casualties, it added.
The Pentagon report said, relations between Afghanistan and Pakistan remain strained but have improved in some areas.
Recent meetings between senior Pakistani and Afghan officials have increased bilateral cooperation, particularly on efforts to achieve a political settlement to the conflict in Afghanistan, it said.
Meanwhile, State Department spokesperson Victoria Nuland has asserted that both Pakistan and Afghanistan sort out their differences through direct dialogue rather than going public.
The statement came amidst sharp exchange of words between Afghanistan and Pakistan over the suicide bombing at the Afghan spy chief.
"We want them to talk it out directly," Nuland said on Monday on being asked about allegations by Afghanistan that the Inter Services Intelligence (ISI) of Pakistan was behind the attack on its spy chief last week.
Pakistan has denied the allegations.
Nuland welcomed the direct talks between Afghan President Hamid Karzai, and his Pakistan counterpart Asif Ali Zardari.
This, she said, will provide opportunity for direct dialogue between the two leaders.
"This, we think, is a good opportunity for them to talk directly about issues of concern rather than sort of doing it by public statement," she said.
"As you know, we have long supported better dialogue between Afghanistan and Pakistan, particularly in support of Afghan-led reconciliation. So we hope that both sides avail themselves of this meeting that the Turks are offering to work through the issues," Nuland said.
US to keep 10,000 troops in Afghanistan post 2014: Report
Soumik, Yashpal help Services post 284 for four vs Goa
US warships not on Libya mission: Pentagon
Pak govt asked to declare Malala as 'Daughter of Pakistan'
Top US commander in Afghanistan under investigation