The Obama administration is open to leaving behind a residual US force when its combat teams leave Afghanistan after America’s longest war at the end of this year.

But it will not do so without legal protections enshrined in the Bilateral Security Agreement (BSA) which Karzai will not endorse.

“President Obama told President Karzai that because he has demonstrated that it is unlikely that he will sign the BSA, the United States is moving forward with additional contingency planning,” a White House statement said.

“Specifically, President Obama has asked the Pentagon to ensure that it has adequate plans in place to accomplish an orderly withdrawal by the end of the year should the United States not keep any troops in Afghanistan after this year.”

The White House had previously warned that Karzai’s intransigence on a deal painstakingly negotiated last year meant it had no choice but to mull the “zero option”.

The statement said Obama was reserving the possibility of concluding a BSA with Afghanistan later this year should the new government be willing.

It was the most concrete sign yet that Washington could wait out the Afghan electoral process before making a final decision on a future role in Afghanistan.

Though Karzai has refused to sign the pact, some candidates to replace him have indicated they would. The deal has also been endorsed by a council of tribal elders.

White House spokesman Jay Carney however said Washington was not certain a future government would sign up.

“I don’t think we would, given the experience we’ve had, predict with any great certainty what might happen,” he said.

“The longer we go without a signed BSA, the more likely a zero option becomes and even if a BSA is signed, the smaller the mission will have to be, by necessity, in scale and ambition.”

Although Afghanistan votes on April 5, a run-off and prolonged horse trading could mean a government is not seated until August – further reducing US planning time.

In Kabul, presidential spokesman Aimal Faizi told reporters the conversation lasted 40 minutes and was friendly.

He said Karzai told Obama the Afghan people wanted the BSA signed – but restated his condition that Washington must first bring the Taliban into peace talks.

US Defence Secretary Chuck Hagel backed Obama’s move, and confirmed for the first time the Pentagon was actively planning a full withdrawal.

Hagel said that Pentagon brass would simultaneously plan options for a prolonged mission in Afghanistan, likely to include at least several thousand US troops.

The row over the BSA is the latest lurch in the deteriorating relationship between Washington and the mercurial Karzai, who was once seen here as a saviour after the toppling of the Taliban but is now viewed as unreliable.

Recently, Karzai’s release of 65 alleged Taliban fighters and warning to Washington to stop “harassing” his judicial authorities further alienated US officials.

The warning to Karzai on Tuesday came hours before Hagel left for Brussels to brief Nato defence ministers on US intentions in Afghanistan.

Obama’s political opponents have warned that leaving Afghanistan without Western troops would strain fledgling national forces stood up by Nato and could lead to a return by the Taliban.

Some have compared such a scenario to Washington’s loss of focus after helping rebels oust Soviet occupiers in the 1980s, leaving a power vacuum exploited by the Taliban, which eventually harboured al-Qaeda as it planned the September 11 attacks in 2001.

Republican Senator John McCain said Obama should deal with a new Afghan government.

“The consequences of us completely pulling out would be the same as we just saw in Iraq: black flags of al-Qaeda flying over the city of Fallujah.”