US President Barack Obama warned his Afghan counterpart, Hamid Karzai, on Tuesday that he is now planning for a full US troop withdrawal because of the Afghan leader’s repeated refusal to sign a security pact.

US President Barack Obama warned his Afghan counterpart, Hamid Karzai, on Tuesday that he is now planning for a full US troop withdrawal because of the Afghan leader's repeated refusal to sign a security pact.

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."