US special forces night raids have increased dramatically in recent months
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Hillary Clinton has defended US Afghan operations against criticism from Afghan President Hamid Karzai.
The US secretary of state said targeted attacks on the networks of militant leaders were a key part of US strategy.
The Afghan leader had told The Washington Post there should be fewer US troops, and called for an end to special forces night raids.
Gen David Petraeus, the coalition commander in Afghanistan, was said to be astonished by Mr Karzai's remarks.
He warned that the Afghan leader's latest public criticism of US strategy threatens to undermine progress in the war, and risked making his own position "untenable", Afghan and US officials told the Washington Post.
'Reduce intrusion'
Mrs Clinton said the military operations were in the best interest of the Afghan people and their government.
"We believe that the use of intelligence-driven, precision-targeted operations against high-value insurgents and their networks is a key component of our comprehensive civilian-military operations," said Mrs Clinton.
"There is no question that they are having a significant impact on the insurgent leadership and the networks that they operate."
She insisted the operations were conducted in full partnership with the government of Afghanistan and pointed out Afghan forces were included on each operation.
Mrs Clinton acknowledged that Washington was sensitive to concerns expressed by President Karzai
But Mrs Clinton acknowledged that Washington was sensitive to concerns expressed by President Karzai, who has been increasingly outspoken about the Western mission.
In his Washington Post interview, he had called on the US to reduce the visibility and intensity of its military operations in the country.
"The time has come to reduce the presence of, you know, boots in Afghanistan... to reduce the intrusiveness into the daily Afghan life," he said.
Calling for a halt to night raids, he said: "I don't like it in any manner and the Afghan people don't like these raids in any manner."
Nato Secretary General Anders Fogh Rasmussen said he respected Mr Karzai's views but did not necessarily agree with them.
'Untenable'
Downplaying the Afghan president's comments on Monday, Waheed Omar, Mr Karzai's spokesman, told news agency AP he had not been criticising the overall strategy, and he had confidence in Gen Petraeus.
Mr Karzai may want the US forces to reduce their footprint, but the BBC's Quentin Sommerville in Kabul says the reality is that Afghan forces simply are not ready to take charge.
Our correspondent adds that there is particular anger from the US side over the president's demand to reduce special forces missions.
The night raids, which have increased dramatically in recent months, are a central plank of Gen Petraeus's strategy to target the Taliban.
But many people would agree that the night raids are deeply unpopular, our correspondent says.
He adds Afghans are also angry that the war against the Taliban has not been won, and that foreign troops have the run of the country.
On Friday, Nato's 28 leaders will begin a two-day summit in the Portuguese capital of Lisbon to discuss handing security responsibility to Afghan forces next year.
Nato hopes for a gradual drawdown of foreign troops from the current peak of about 150,000 soldiers from more than 40 countries.
US President Barack Obama sent an additional 30,000 troops to Afghanistan last year, raising the level of American troops there to almost 100,000.
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