Finding Kerstin seriously ill, doctors appealed for her mother, who at that time was assumed to be missing, to come forward to provide more details about her medical history.
Josef F allegedly then released the mother and two other children from the cellar, telling his wife Rosemarie that she had chosen to return home, police say.
It was not immediately clear how police were alerted.
The mother, named as Elisabeth F, has been receiving medical and psychological treatment since being discovered.
She appeared "greatly disturbed" psychologically during questioning and agreed to talk only after authorities assured her that she would no longer have to have contact with her father, and that her children would be taken care of, police added.
The six children are three boys and three girls aged between five and 20.
Police spokesman Franz Polzer told reporters they were now all in "psychological care in a secure institution in a clinic here in this area".
"They are being cared for individually - those between 12 and 16 years of age who grew up with their grandparents, and two boys who, when they came out yesterday with their mother, saw the daylight for the first time in their lives," he said.
Police said three of the children were registered with authorities and lived with the grandparents.
According to police, Josef F and wife Rosemarie had told authorities the three had been abandoned at birth outside their home - in 1993, 1994 and 1997 - each time, the couple claimed, with a note from Elisabeth saying she could not care for the babies herself.
'Dead baby burnt'
The police issued a statement giving details of the alleged abuses Elisabeth recounted to them.
She said she had been sexually abused by her father since the age of 11.
Josef allegedly lured her into the cellar of their house in Amstetten on 28 August 1984, drugging and handcuffing her before locking her up.
It was assumed she had disappeared voluntarily when her parents received a letter from her asking them not to search for her.
"Abused continuously during the 24-year-long imprisonment", Elisabeth bore six children while a seventh, one of a set of twins, died soon after birth.
The dead baby was allegedly taken out of the cellar and burnt by Josef.
Elisabeth said Josef had provided her and three of her children, who were locked up along with her, with clothing and food.
His wife Rosemarie had allegedly not been aware of what was going on.
The discovery of another Austrian woman, who was held captive in a cellar by an abductor for more than eight years, gripped the country in 2006.
Natascha Kampusch finally escaped from her kidnapper, 44-year-old Wolfgang Priklopil, who killed himself shortly afterwards.
Ms Kampusch was abducted at the age of 10 in 1998 and held in a small, windowless cellar beneath Priklopil's garage in the commuter town of Strasshof, near Vienna.
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