Mr Karzai said the growing number of raids, some of which are carried out by Britain's SAS, was aggravating Afghans and their anger may strengthen the Taliban-led insurgency.
The Afghan president has repeatedly criticised Nato tactics.
Coalition commanders have hailed the summer's unprecedented campaign of special forces operations to kill or capture insurgent figures as a potent weapon against the Taliban.
Intelligence reports suggest Taliban commanders inside Afghanistan are harried and have complained to their leadership they have constantly to change their locations.
More than 300 insurgent leaders have been captured or killed in the past three months Nato has claimed.
Several botched assaults have caused civilian deaths however and complaints of arbitrary detention or raids based on faulty intelligence are widespread in southern Afghanistan.
Mr Karzai said: "I don't like it in any manner and the Afghan people don't like these raids in any manner.
He told the Washington Post: "We don't like raids in our homes. This is a problem between us and I hope this ends as soon as possible... Terrorism is not invading Afghan homes and fighting terrorism is not being intrusive in the daily Afghan life."
Nato officials have about 1,000 special forces operations are taking place each month, surpassing the campaign which destroyed the al Qaeda leadership in Iraq.
"The time has come to reduce military operations," Mr Karzai said. "The time has come to reduce the presence of, you know, boots in Afghanistan ... to reduce the intrusiveness into the daily Afghan life."
A spokesman for the Nato-led coalition said raids were carried out in cooperation with the Afghan authorities.
"There is no question that they are having a significant impact on insurgent leadership and its networks", he said.