Televised remarks on Sunday from Karzai suggesting that the US depended on insurgent Taliban attacks to justify its presence in Afghanistan forced Hagel and NATO's regional force commander, US General Joseph Dunford, to issue flat denials.
"We have shed too much blood over the past 12 years...to ever think that violence or instability would be to our advantage," said Dunford. "It's categorically false."
Hagel said after his private talks with Karzai that he had told the president that it was "not true that the United States was unilaterally working with the Taliban."
"The fact is any prospect for peace or political settlements, that has to be led by the Afghans," Hagel added. "He has his ways," said Hagel, referring to Karzai's behavior.
Their joint appearance in front of the cameras was to have been a key event during the newly inaugurated Pentagon chief's visit to Afghanistan.
Karzai, in his speech on Sunday marking Women's Day, claimed that two bombings on Saturday had "served" America by scaring Afghans into thinking that without US-led forces beyond their planned pullout in 2014 "our people will be eliminated."
Nineteen people were killed by Saturday's two bombings – one within Hagel's earshot in Kabul and the other in Khost.
Remarks coincide with watershed talks
Washington and Kabul are currently negotiating terms for a security agreement that would allow the US to maintain a military presence beyond 2014. Currently, 96,000 US-led NATO combat troops are deployed in Afghanistan.
Any foreign troops remaining in Afghanistan "must respect Afghan laws and the national sovereignty and our customs," Karzai said.
The planned transfer of the controversial Bagram jail near Kabul from US to Afghan control due on Saturday was also delayed because of last-minute disagreements, said officials from sides.
The US fears that some detained Afghans would return to insurgency. Karzai has said Bagram's detainees are innocent.
Karzai on Sunday also issued a decree banning international forces from entering university grounds after alleged harassment of students.
That assertion was denied by Dunford who also declined to say when US special forces would leave Wardak province despite a deadline set by Karzai two weeks ago. It expired on Sunday.
"Transitions are tough," Dunford said. "Our relationship is changing, it's maturing, we're moving into support as they move into the lead and we're going to have to grind through issues as they occur."
Renewed US-Taliban talks denied
The US embassy in Kabul also rejected a Karzai assertion that the Taliban had been holding talks with the United States on a "daily basis."
Embassy spokesman David Snepp said the Taliban "suspended talks with the US in March 2012."
"It's up to the Taliban to take the next steps. They know what they need to so," Snepp said.
Taliban spokesman Zabihullah Mujahid denied that such talks had been resumed.
"The Taliban strongly rejects Karzai's comments," Mujahid said.
ipj/hc (AP, dpa, AFP; Reuters)