The men, members of the minority Hazara ethnic group, were taken on Monday evening in Zabul province, on the road between the western city of Herat and the capital Kabul.
Hazara Shiite Muslims are often the target of violence at the hands of extremists in Pakistan and Afghanistan.
"Our driver saw a group of masked men in Afghan army uniform signalling him and he thought they were soldiers so he stopped," said Nasir Ahmad, an official with the Ghazni Paima bus company, told AFP.
"The gunmen took 30 Hazaras away with them."
Ahmad said the kidnappers took only the men on the two buses and released the women and children travelling with them, AFP reported.
No one immediately claimed responsibility for the abduction, but kidnappings for ransom by bandits, local militias and the Taliban are common in Afghanistan.