The president's remarks follow a recent strike that mistakenly killed a group of children and women in southern Helmand province. He said it would be the last.
"From this moment, airstrikes on the houses of people are not allowed," Karzai told reporters in Kabul.
NATO says it never conducts such strikes without Afghan government coordination and approval. A spokesman for NATO forces in Afghanistan said they will review their procedures for airstrikes given Karzai's statement but did not say that it would force any immediate change in tactics.
"In the days and weeks ahead we will coordinate very closely with President Karzai to ensure that his intent is met," spokeswoman Maj. Sunset Belinsky said. Karzai has previously made strong statements against certain military tactics — such as night raids — only to back off from them later.
But if Karzai holds to what sounds like an order to international troops to abandon strikes, it could bring the Afghan government in direct conflict with its international allies.
"Coalition forces constantly strive to reduce the chance of civilian casualties and damage to structures, but when the insurgents use civilians as a shield and put our forces in a position where their only option is to use airstrikes, then they will take that option," Belinsky said.
It is unclear if Karzai has the power to order an end to such strikes. NATO and American forces are in Afghanistan under a United Nations mandate that expires in October. The United States is negotiating an agreement with the Afghan government on the presence of its forces in the country going forward, but this has already become contentious, with Karzai declaring that he will put strict controls on how U.S. troops conduct themselves in his country.
"The Afghan people can no longer tolerate these attacks," Karzai told reporters at the presidential palace.
He issued a veiled threat: "The Afghan people will be forced to take action." He did not, however, say what this action would be.
Karzai said that NATO forces risk being seen as an "occupying force" if they continue with their current approach, using the same phrase that Taliban insurgents use to describe the international coalition.
"We want it to be clear that they are working in a sovereign nation," Karzai said.
At least nine civilians were killed in the air strike in Helmand province on Saturday, according to NATO figures. Afghan officials have said 14 were killed, including at least 10 children and two women.
NATO officials have apologized for the strike on two houses in Nawzad district, saying their troops thought there were only insurgents inside the targeted compound when they ordered the strike.
Southwest regional commander U.S. Marine Maj. Gen. John Toolan said that the airstrike was launched after an insurgent attack on a coalition patrol in the district killed a Marine. Five insurgents occupied a compound and continued to attack coalition troops, who called in an airstrike "to neutralize the threat," Toolan said.
The troops later discovered there were civilians inside the house.
Karzai has vacillated between calling for an end to airstrikes and night raids and softer rebukes of NATO forces, telling them they have to exercise more caution. NATO has managed to significantly reduce civilian casualties from its operations in recent years.
Meanwhile, civilians deaths from insurgent attacks have spiked.
At least 2,777 civilians were killed in Afghanistan in 2010, a 15 percent increase over the prior year, according to a United Nations report. The insurgency was blamed for most of those deaths, and while civilian deaths attributed to NATO troops declined 21 percent in 2010, Afghan leaders say the number remains too high.