Zahir Tanin's statement to the UN Security Council was sharply at odds with Afghan President Hamid Karzai's final address to parliament on Saturday ahead of April 5 presidential elections.
Karzai reiterated he would not sign the agreement and said US soldiers could leave on schedule because his military, which already protects 93 percent of the country, was ready to take over entirely.
"To this end, we are certain the Bilateral Security Agreement with the United States will be signed soon," Tanin said.
The US force would train and mentor Afghan troops, and some US Special Forces would also be left behind to hunt down al-Qaeda.
All 10 candidates seeking the presidency have said they would sign the security agreement.
Jan Kubis, the top UN envoy in Afghanistan, told the council the election will mark the first democratic transfer of power in Afghanistan's history and he urged all citizens to vote and not let "spoilers and terrorists deprive you of your choice, of your future."
Kubis said he is "gravely disturbed" at the Taliban's recent declaration that it will seek to disrupt the election process by "unleashing a campaign of terror."
He said a breakthrough in direct talks between the Afghan government and Taliban "remains elusive so far despite some interesting recent initiatives by the High Peace Council," which he did not disclose.
Kubis called for continued patient efforts to build "an environment conducive to more formal efforts later, where the United Nations should, and would, have a more prominent role."
Speaking after the vote, US deputy ambassador Rosemary DiCarlo did not comment on the unsigned agreement with Afghanistan but she said "serious security threats remain in Afghanistan."
"A successful transfer of presidential power this year following democratic elections will solidify the gains made over the past 12 years and contribute much to the country's future development and stability," DiCarlo said.
"It will also show all Afghans including the Taliban that the rule of law matters, and that Afghanistan's constitutional system is resilient enough to overcome grave obstacles.
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