"Part of the insecurity is coming to us from the structures that NATO and America created in Afghanistan," Karzai told NBC News during an interview at the presidential palace in Kabul.
He also recognized that much of the country's violence was caused by insurgents.
Karzai, now in his second five-year presidential term, also told NBC News he told President Obama in a letter Afghanistan would not sign any new security pacts with the United States until hundreds of prisoners in U.S. custody were transferred to Afghan authorities.
"I have written to President Obama that the Afghan people will not allow its government to enter into a security agreement, while the United States continues to violate Afghan sovereignty and Afghan loss," he said.
His criticism of the United States comes after the beginning of bilateral talks on a security accord concerning the role the United States would play after most of its troops are withdrawn by the end of 2014.
Karzai said detainees in U.S. custody in Afghanistan were being held in violation of an agreement he and Obama signed in March.
"We signed the strategic partnership agreement with the expectation and the hope ... the nature of the United States' activities in Afghanistan will change," Karzai said.
Karzai also told NBC News that he didn't think al-Qaida "has a presence in Afghanistan."
"I don't even know if al-Qaida exists as an organization as it is being spoken about," he said. "So all we know is that we have insecurity."