The local Pamir Airways flight disappeared off the radar, on the way between the capital Kabul and Kunduz in the north of the country. It had 38 passengers and five crew members.
The model of the aircraft was not immediately clear, said the spokesman of the ministry. There were also some foreigners on board.
"We can confirm that a plane has crashed over the Salang mountains with 38 passengers and five crew members on board," the interior ministry spokesman Zemarai Bashary informed the media.