"When the Taliban entered the hospital they killed 35, all civilians," spokesman Shah Hussain Murtazawi said, without specifying if they were patients or staff. "This is a cruel crime against humanity."
He did not elaborate, but unconfirmed reports Sunday claimed that the Taliban had set the hospital alight and killed those inside.
The Taliban have denied the claim, though a spokesman said that parts of the local hospital were damaged in fighting in the area.
It came as the insurgents captured Taywara district in Ghor province after days of fighting, the latest victory by the resurgent militants.
But the insurgents have ramped up their offensive across the country since launching their so-called "spring offensive" earlier this year.