The US intelligence chief said Tuesday he does not expect Afghan President Hamid Karzai to sign a security agreement with the United States that would allow American troops to stay after 2014.

Washington has repeatedly appealed to Karzai to sign the bilateral security agreement (BSA) negotiated last year but James Clapper, director of national intelligence, said he had given up hope that the Afghan president would endorse the deal.

"Well, obviously, it takes two to sign this," Clapper told the Senate Armed Services Committee.

"And it's my own view, not necessarily company policy, ...I don't believe President Karzai is going to sign it," he said.

His comments were the most explicit yet by a senior US official acknowledging the bleak prospects of Karzai backing the agreement.

Senator Carl Levin, chairman of the committee, asked Clapper if it would be better for the US government to wait for the next Afghan president to sign the deal after the country's April elections.

Clapper said that would be a policy decision and not up to him but he said such a move could "have a salutary effect."

The United States favors leaving about 10,000 troops in Afghanistan after this year to help train Afghan forces and counter Al-Qaeda militants and its allies.

The delay in signing the security agreement, which would set up a legal framework for foreign troops to stay post-2014, has created uncertainty and undermined confidence among Afghans, Clapper said.

"The effect already of the delay has been negative in terms of the impact on the economy, not to mention I think the psychological impact," he said.

Worries about whether NATO-led forces will remain in the country have triggered negative trends in the economy, including a decline in foreign investment, he said.

Asked about the state of Afghan forces as NATO troops draw down, Clapper said the country's army has improved but suffers from "extensive desertion problems."

About 30,000 Afghans deserted last year out of an army of 185,000, the intelligence chief said.

On the battlefield, Afghan forces often score tactical victories against Taliban insurgents but have difficulties holding cleared territory, particularly when police units are involved, he said.

The head of the Defense Intelligence Agency, Lieutenant General Michael Flynn, told the same hearing that Afghan troops have made "modest progress" but still need international assistance with logistics, air transport and intelligence.

If a small US-led contingent remains in Afghanistan after the end of the year, special operations forces will form the backbone of the force.

The head of special operations command, Admiral William McRaven, said at a separate event on Tuesday that the US military had a crucial role to play in Afghanistan, including advising Afghan troops and conducting counter-terrorism operations.

"No matter the size of our presence there next year, our future mil-to-mil (military to military) engagement with the Afghans will remain vital in the region," he said.