Karzai said this week that he was prepared to walk away from the Bilateral Security Agreement (BSA) talks if Afghanistan was not happy with its conditions.
The US has repeatedly pressed for the pact to be signed by the end of this month, so that the US-led NATO military coalition can schedule its withdrawal of 87,000 combat troops by December 2014.
"President Obama and President Karzai reaffirmed both back in January that the goal here was to complete the BSA in October," a state department official travelling with Kerry told reporters.
"Uncertainty about an incomplete BSA could erode the resolve among NATO allies, makes (it) more difficult to plan for the US, makes (it) more difficult to plan for our NATO allies."
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Karzai has said he refuses to be rushed into signing the deal, and would first seek approval from a traditional grand assembly of tribal leaders to be convened in about month's time.
"If it doesn't suit us and if it doesn't suit them, then naturally we will go separate ways," he said in a BBC interview broadcast on Monday.
According to the Afghan government, talks ground to a halt over US demands for the right to conduct unilateral military operations, and on how the US would pledge to protect Afghanistan.
The collapse of a similar agreement with Iraq in 2011 led to the US pulling its troops out of the country, which is currently suffering its worst sectarian violence since 2008.
But Kabul has dismissed the possibility that the US may enact the "zero option" of a complete pull-out after its soldiers have fought the Taliban since the 9/11 attacks in 2001.