A top Pentagon official said Friday it would be a "tragedy" if Afghan and US negotiators failed to clinch a deal allowing US troops to stay in the country after 2014.

Deputy Defense Secretary Ash Carter said he told leaders in Kabul during a visit earlier this month that President Barack Obama wanted to see a bilateral security agreement wrapped up as soon as possible to provide "certainty" to commanders.

"We need that soon because we need to be able to plan. And we need it soon because our allies and partners need to be able to plan," Carter told AFP and other newswire services in an interview.

"It would be a tragedy if this thing wasn't concluded soon, because most Afghans are in favor of the coalition continuing its work there to strengthen the Afghan forces so they can go on and live a better life."

His comments reflected growing impatience in Washington as the talks on a security agreement have dragged with pivotal Afghan elections looming as well as the departure of NATO troops.

Carter also said the US government still viewed October as the target date for clinching the post-2014 security accord, a timeline favored by US commanders as they manage a massive withdrawal of troops and equipment.

"We need certainty... just from a military planning point of view," Carter said.

The United States plans to pull out the bulk of its 57,000 troops in Afghanistan by the end of 2014 and has tentative plans to retain a smaller force of around 10,000 forces after that.

But a new security agreement is needed to allow for the post-2014 presence, including provisions allowing the United States access to various bases.

Carter said the negotiations had made progress and the remaining disagreements were not insurmountable.

"I think it's down to the point where the issues that remain are very well-defined, (and) I think are very resolvable and it just takes an act of will to carry it across the finish line," he said.

He declined to disclose the remaining unresolved issues.

Afghan President Hamid Karzai has told Washington he is seeking to secure "broad support" for the security deal and therefore needs time to organize a loya jirga, or large assembly, that would debate the agreement, according to Carter.

A security accord would send an important symbolic message to reassure Afghans and countries in the region, while making it clear to Taliban insurgents that the only way forward is to pursue peace talks, he added.

The Pentagon's number two civilian leader also said disputes that had previously held up the withdrawal of US equipment out of the country through Pakistan were "by and large" resolved.

"The big gridlock on the Pakistan groundlines of communication, both on the Pakistani side and the Afghan side, has been eliminated and things are flowing," said Carter, who paid a three-day visit to Afghanistan this month before heading to India and Pakistan for talks.

But he acknowledged some minor problems as "there's always somebody at some border post that hasn't gotten the word."

The Afghan government shut the border earlier this year in a dispute over what the US military should pay for withdrawing its gear, with Kabul insisting the Americans owed up to $70 million in customs fines.

Washington maintained that the military equipment came into the country legally and refused to pay the fees. Afghan authorities eventually reopened the border.