Officials said Gen Petraeus voiced “astonishment and disappointment” at Mr Karzai’s demand he should reduce the number of night raids searching for insurgents.
Mr Karzai’s attack on a cornerstone of Gen Petraeus’s strategy “is really undermining [Petraeus’s] endeavours”, one foreign diplomat told theWashington Post.
The latest row in the fractious relationship between Mr Karzai and his foreign backers was triggered by his comments in a weekend interview that “the time has come to reduce military operations”.
The Afghan president singled out this summer’s unprecedented special forces campaign of raids, some carried out by Britain’s SAS, targeted at insurgent commanders and bomb-makers.
He said: “I don’t like it in any manner and the Afghan people don’t like these raids in any manner.
“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.” Gen Petraeus, reacted on Sunday by making what witnesses described as “hypothetical” references to his inability to continue operations in the face of Mr Karzai’s remarks, during a meeting with senior Afghan officials, the newspaper said.
He did not attend a scheduled meeting with the Afghan president, who himself cancelled a press conference by his spokesman.
Western diplomats are regularly exasperated by Mr Karzai’s unpredictable outbursts and the dispute follows friction on his decision to ban private security companies and his insistence most corruption is caused by foreigners.
Relations had recently improved he said in the same interview and “we don’t shout at each other as often as we did before”.
Afghan officials seeking to smooth over the row denied Mr Karzai’s comments were a vote of no confidence in America’s senior general in Afghanistan, the paper said.
Special forces teams are carrying out more than 1,000 raids a month and intelligence reports suggest Taliban commanders inside Afghanistan are harried and must constantly 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.