The incident has spotlighted rampant child labour in the country. After social media images allegedly showing injuries to the girl's face and hands went viral, the top court intervened last week and ordered a full investigation.
The court also demanded police find the child, who is not being named by AFP. Her father removed her from a women's shelter amid reports he had forgiven the judge and his wife and described his daughter's story as untrue.
"She shows signs of torture," Javed Akram, head of the Pakistan Institute of Medical Sciences hospital, told AFP.
"Our medical board has observed multiple injuries, burns, blunt injuries and bruises on the child's face," he said.
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"She has burn marks on her back and on the left hand. She also has a blunt wound on her face. All her wounds are healing."
Another doctor said on condition of anonymity that the child, employed by a district judge in Islamabad, had changed her statement several times.
Current figures on the scale of child labour in Pakistan are not available. According to Human Rights Watch, about 13 percent of Pakistani children aged 10-14 are working.