"We all know the facts," NATO chief Anders Fogh Rasmussen said.
"If there is no US-Afghan agreement, there can be no NATO-Afghan deal. And if there is no agreement, there will be no NATO troops in Afghanistan after 2014," Rasmussen said as he went into a NATO defence ministers meeting.
"Let me stress, this is not our preferred outcome," he said. "But these are the facts, facts that we need to take into account in our planning.
"This is why I once again urge Afghan leaders to sign the security agreement with Washington,” he added.
Rasmussen spoke after US President Barack Obama told his Afghani counterpart Hamid Karzai that he was now planning for a full US troop withdrawal because of Kabul's repeated refusal to sign the security pact.
The deal would lay down the legal basis for a continued US and NATO troop presence in the form of a training mission post-2014.
It is expected to number up to 12,000 troops, mostly American, and is seen as an important guarantee of continued US and NATO support during a difficult transition period.
In 2011, Washington withdrew all its forces from Iraq when it could not secure an agreement with Baghdad. There are fears a similar outcome in Afghanistan could leave the way clear for the Taliban to return to power.
Karzai says he will not sign the accord until after the April presidential election.
Significantly, Rasmussen said NATO was "ready to engage with a new president" if need be.
Several Afghan presidential candidates have indicated they would sign, and the deal has also been endorsed by a council of tribal elders.
White House spokesperson Jay Carney said on Tuesday that Washington was not certain a future government would do the deal.
"I don't think we would, given the experience we've had, predict with any great certainty what might happen," he said.
Hagel to attend NATO meeting
US Secretary of Defence Chuck Hagel announced on Wednesday that he will attend the NATO defence minister's meeting scheduled for February 27, 2014.
In a statement released on Wednesday, Hagel, who is currently visiting military bases in Virginia, will be travelling for the meeting where the presence of troops in Afghanistan will be top of the agenda.
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