The brazen suicide car bombing in Logar province, about 75 kilometres south of the capital Kabul, also wounded over 20 people and officials warned the death toll could still rise.
It was condemned "in the strongest terms" by the United Nations, which said the hospital's maternity ward was badly damaged in the attack and many of the victims were women and children.
Underlining the confusion and chaos at the site, the ministry of public health initially put the death toll at 60 but later corrected its own figures.
An eyewitness described horrific scenes of victims on fire and body parts scattered in all directions following the blast in the remote district of Azra, close to the border with Pakistan.
"At least 20 of our countrymen have been martyred and around 25 are wounded," the ministry said, strongly condemning the attack.
The Afghan interior minister also said that 20 people were killed including hospital staff and patients, while 23 civilians were wounded.
But provincial health director Mohammad Zaref Nayebkhail told AFP the death toll could still be significantly higher as many people came to the scene quickly after the blast and removed the bodies of their relatives.
Din Mohammad Darwaish, the Logar provincial spokesman, said the attack was a suicide car bombing.
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