The move by Hamid Karzai could derail the peace process even before it has begun.
In a terse statement from his office, Karzai said negotiations with the U.S. on what American and coalition security forces will remain in the country after 2014 have been put on hold.
The statement followed an announcement Tuesday by the U.S. and the Taliban that they would pursue bilateral talks in Qatar before the Afghan government was brought in.
"In view of the contradiction between acts and the statements made by the United States of America in regard to the peace process, the Afghan government suspended the negotiations, currently underway in Kabul between Afghan and U.S. delegations on the bilateral security agreement," Karzai's statement said.
His spokesman was not immediately reachable for questions, and the U.S. Embassy in Kabul said nobody was available for immediate comment.
Though the Taliban have dismissed Karzai as an American puppet for years, they indicated Tuesday when opening a new political office in Doha, Qatar, that they would be willing to talk with the Afghan leader.
But both the American side and the Taliban said they would first meet together before any talks with the Afghanistan government.
In another incident highlighting the fragile situation in Afghanistan, only hours after announcing they would hold talks with the U.S., the Taliban claimed responsibility Wednesday for an attack on the Bagram Air Base in which four American troops were killed.
Taliban spokesman Zabiullah Mujahid said the insurgents fired two rockets into the base outside the Afghan capital, Kabul, late on Tuesday. American officials confirmed the base had come under attack by indirect fire — likely a mortar or rocket — and that four U.S. troops were killed.
Also Tuesday, five Afghan police officers were killed at a security outpost in Helmand province by apparent Taliban infiltrators — the latest in a string of so-called "insider attacks" that have shaken the confidence of the nascent Afghan security forces.
The opening of a Taliban political office in Doha with the intention of starting peace talks was a reversal of months of failed efforts to start negotiations while Taliban militants intensified a campaign targeting urban centres and government installations across Afghanistan.
President Barack Obama cautioned that the peace talks with the Taliban would be neither quick nor easy but that their opening a political office in Doha was an "important first step toward reconciliation" between the Islamic militants and the government of Afghanistan.
In setting up the office, the Taliban said they were willing to use all legal means to end what they called the occupation of Afghanistan — but did not say they would immediately stop fighting.
American officials said the U.S. and Taliban representatives will hold bilateral meetings in the coming days. Karzai's High Peace Council had been expected to follow up with its own talks with the Taliban a few days later but it was now not clear whether that would happen.
The Taliban announcement followed a milestone handover in Afghanistan earlier Tuesday as Afghan forces formally took the lead from the U.S.-led NATO coalition for security nationwide. It marked a turning point for American and NATO military forces, which will now move entirely into a supporting role.
The handover paves the way for the departure of the majority of coalition forces — currently numbering about 100,000 troops from 48 countries, including 66,000 Americans — within 18 months.
The NATO-led force is to be cut in half by the end of the year, and by the end of 2014 all combat troops are to leave and be replaced — contingent on Afghan governmental approval — by a smaller force that would be on hand for training and advising.
It was not immediately clear how long Karzai planned to suspend the negotiations on the agreement.
The U.S. has not yet said how many troops will remain in Afghanistan, but it is thought that it would be a force made up of about 9,000 Americans and 6,000 allies.
Six years ago, Afghan security forces numbered fewer than 40,000, and have grown to about 352,000 today. But questions remain if they are good enough to fight alone.
In the Helmand attack late Tuesday, local official Mohammad Fahim Mosazai said five police officers who had only been on the local force for three months were killed, apparently by five of their fellow officers. He blamed the killings on Taliban infiltrators, and said the suspects escaped with the victims' weapons.
In a similar attack in Helmand a week ago, six policemen were found shot dead at their checkpoint, and there have been several other such incidents in the past year, including officers poisoned while eating.
Taliban insurgents have warned they would infiltrate Afghan security forces to carry out insider attacks.
Overnight in the eastern province of Nangrahar, police ambushed Taliban fighters outside a village in the Surkh Rod district, killing four and capturing two militants. Two police officers were wounded in the fighting, said deputy provincial police chief Masoon Khan Hashimi.