It said one of the commanders was involved in smuggling suicide attackers, foreign fighters and weapons into neighbouring Afghanistan.
The raids took place at two compounds 10 km southwest of Khost city after intelligence indicated militant activity at those locations, the statement said.
In Ghazni province, several militants were killed Thursday night after they opened fire on troops arriving to raid a compound in the Giro district, another US statement said. Some militants who fled the raid were also killed.
The US military said the aim of the operation was to disrupt the Taliban's operational and logistical support network for ambushes.