The insurgents were plotting to use the camps as staging bases for attacks aimed at disrupting legislative elections this month, the military said in a statement on Tuesday.
The raids occurred in Zabul province on Monday. Nine suspected insurgents were also detained, it said.
"We were engaged as soon as we got off the helicopters," Sergeant-Major Bradley Meyers, from the 2nd Battalion 503rd Infantry (Airborne), was quoted as saying. "We returned fire, and the enemy fell, one by one."
Multinational force warplanes and attack helicopters also took part in the fighting, it said. After the battle, troops found various bomb-making materials at the site.
The Afghan and multinational forces suffered no casualties.
The fighting came a day after 200 Afghan police personnne, supported by US-led forces, killed 13 suspected Taliban fighters in southern Afghanistan and rounded up more than 40 others.
Kandahar governor Asad Allah Khalid said the deaths occurred after a gun battle on Sunday night during a campaign to remove fighters from the Ghorak district in southern Kandahar province.
Thirteen suspected fighters were
killed in the south on Sunday
"We have the dead bodies," Khalid said, referring to the slain Taliban fighters. He said 44 other suspects were arrested and assault rifles and some ammunition were confiscated.
US military spokesman Colonel James Yonts confirmed that more than 40 suspected insurgents had been detained. He said some may be released after questioning.
He gave no details on casualties pending completion of the operation, which follows a spate of guerrilla-style strikes in southern provinces over the weekend.
More than 1100 people have been killed in the past six months, and US military commanders believe the violence may worsen in the run-up to the legislative elections on 18 September.
The US military said nine other suspected insurgents were detained in a two-week operation that ended on Friday in the eastern province of Paktika.
They included "four suspected leaders and advisers of a criminal cell", arrested with "Taliban propaganda on audio tapes" and three others linked to a bomb-making cell.