The accusation came from Ahmad Eshchi, the former governor of General Dostum's home province of Jowzjan in the north.
He said the vice-president and 10 other men assaulted him while he was forcibly kept at the former warlord's residence for five days late last month.
Gen Dostum denied the accusation, describing it as a "provocation".
He said Mr Eshchi was detained not by him, but by the country's intelligence service.
