But in a rare telephone call with President Karzai, Obama also held out the possibility of agreeing a post-2014 training and anti-terror mission with the next government in Kabul.
The US threat was the latest twist in a long political struggle with Karzai, who appears intent on infuriating Washington until the day he leaves office, sometime after elections in April.
The Obama administration said its preferred option is to leave behind a residual US force when its combat teams depart 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) agreed between the two governments, 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, detailing the call. "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 2014."
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 do so. 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 be on board. "I don't think we would, given the experience we've had, predict with any great certainty what might happen," he said, betraying US impatience with the situation. "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 horsetrading could mean a government is not seated until August – further reducing US planning time.
In Kabul, presidential spokesman Aimal Faizi said the conversation lasted 40 minutes and was friendly. He said Karzai told Obama that Afghans wanted the BSA signed – but restated his condition that Washington must first bring the Taliban into peace talks.
US Defense Secretary Chuck Hagel backed Obama's move, and confirmed for the first time the Pentagon was actively planning a full withdrawal. He said Pentagon brass would simultaneously plan options for a prolonged mission in Afghanistan, likely to include at least several thousand US troops.
The call between Karzai and Obama came hours before Hagel left for talks with NATO defense ministers in Brussels, at which he will share US planning on its future Afghan role.
The row over the BSA is the latest lurch in the deteriorating relationship between Washington and the mercurial Karzai, who was once seen as a savior 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.
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, who ruled Afghanistan from 1996 to 2001. 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 harbored 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."