The report from the Central Forensic Sciences Laboratory (CFSL) here, which was submitted before a trial court this week, has pointed out that the DNA sample of the delivered child and the alleged rapist, maternal uncle, did not match.
The DNA mismatch in the CFSL report has been confirmed by the defence lawyer.
The girl had told her parents and police investigators earlier that her maternal uncle - a cousin of her mother - had raped her. She had identified the accused later.
Police sources said that two women police officers had spoken to the child victim but had not been able to gather much information.
A senior woman police officer from the Chandigarh Police is likely to meet the victim soon.
The court has listed the matter for hearing on Friday.
The girl's pregnancy was only discovered in July after her parents took her to hospital when she complained of stomach pain. They discovered that the girl had been repeatedly raped by her uncle over seven months.
The maternal uncle, aged around 45 years, was arrested and is undergoing trial in the matter.
A medical board, set up by Chandigarh's Postgraduate Institute of Medical Education and Research (PGIMER) on the apex court's orders to examine the pregnant child, had warned that an abortion would risk the girl's life.
The order came on a PIL by advocate Alok Srivastava who moved the top court after a plea for the medical termination of pregnancy was refused by a district court in Chandigarh on July 18.
The plea contended that the victim's body was not ready for childbirth.