Mullah Naqibullah, the commander of Taliban's militia in Kandahar and his close colleague Mullah Abdul Qayum were reportedly among those arrested.
"We took into custody three Taliban leaders but cannot disclose their names," Salim Khan, the Deputy Intelligence Chief of Kandahar told Xinhua via telephone.
Afghan officials in Kabul and US military refused to confirm the arrests while the spokesman of Defense Ministry Zahir Azimi said that Afghan National Army (ANA) was not involved in this operation.
Another eight suspected Taliban fighters were arrested in the neighboring Uruzgan province early last week, Xinhua said.