The operation, described by some Western media as the first ground raid by U.S.-led forces on Pakistani territory, occurred Wednesday near Angoor Adda in South Waziristan near the border with Afghanistan.
"The government of Pakistan strongly condemns the assault by coalition ... troops on a village near Angoor Adda inside Pakistani territory, which has resulted in immense loss of civilian life," the state-run Associated Press of Pakistan quoted Pakistani Foreign Ministry spokesman Muhammad Sadiq as saying.
The International Herald Tribune, quoting U.S. officials, said the assault was against al-Qaida militants, making it the first publicly acknowledged U.S. ground raid on Pakistani soil.
CNN quoted a senior U.S. official as saying a small number of U.S. helicopters landed troops in an area where Taliban and al-Qaida fighters had found refuge over the years, seeking targets linked to recent attacks on U.S. troops in Afghanistan.
A separate APP report, quoting the provincial government, said the shelling of Angoor Adda killed at least "20 innocent people," including women and children.
Pakistani Prime Minister Yousaf Raza Gilani was quoted as saying no external forces could be allowed to launch an attack in Pakistan's territory.
Pakistan's Dawn reported U.S. Ambassador Anne Patterson was summoned to the foreign office to receive Pakistan's protest.