The girls were found hanged from a tree in Uttar Pradesh state in May, in a case which sparked global outrage.
Three suspected attackers were taken into custody along with two policemen.
At the time a local post-mortem examination confirmed multiple sexual assaults and death due to hanging.
The case was initially investigated by the state police, but later handed over to federal investigators at India's Central Bureau of Investigation (CBI).
Correspondents say it is not clear how the CBI will be able to resolve the apparent contradictions between the latest forensic conclusions and the earlier post-mortem performed by the local authorities.
The father of one of the victims said he was shocked by the latest report.
"I don't know whether the samples sent to the labs were of my daughter or of someone else. Ever since the post-mortem was conducted every effort has been made to conceal the facts... Justice is being denied to us," he said.
Last month, the CBI attempted to exhume the bodies of the girls but their graves were under floodwaters and remain inaccessible to this day.
But India's Centre for DNA Fingerprinting and Diagnostics (CDFD) was able to examine the clothes and personal effects of the two girls and reported that it found no proof of sexual assault, a CBI spokesperson told BBC Hindi.
The CBI refused to provide any more details, but media reports quoting sources in the CDFD said "no male DNA had been found on the clothes and personal effects" of the girls and also "no female DNA was found on the samples taken from the male suspects".
The Indian Express reported that the laboratory analysed "items of clothing" and personal effects worn by the two victims as well as the clothes worn by the accused. It also said that blood samples and swabs from both the victims and the accused were examined.
The story of the hangings of two teenage cousins in a north Indian village is getting murkier with each passing day.
The initial reports said the lower-caste girls had been gang raped and hanged by young men from a slightly higher caste.
A post-mortem carried out on the girls by a team of three local doctors in Badaun said the girls had injuries "suggestive of rape".
Three men were arrested, along with two policemen, and remain in jail nearly three months after the crime.
But in recent weeks, reports being leaked by the investigators to Indian media have turned the story on its head.
Officials are now raising questions about the testimony of the victims' families - they say lie-detector tests done on the girls' families indicate "deception".
Questions have also been raised about the credibility of the main witness, a neighbour of the girls.
Some reports have said the murders may even be a case of honour killing.
All such reports have been vehemently denied by the family.
But the latest round of revelations from the CDFD has added a further twist to the tale
How federal investigators will reconcile the contradictory reports of the two major forensic investigations is as yet unclear.
Three suspected attackers were taken into custody along with two policemen.
At the time a local post-mortem examination confirmed multiple sexual assaults and death due to hanging.
The case was initially investigated by the state police, but later handed over to federal investigators at India's Central Bureau of Investigation (CBI).
Correspondents say it is not clear how the CBI will be able to resolve the apparent contradictions between the latest forensic conclusions and the earlier post-mortem performed by the local authorities.
The father of one of the victims said he was shocked by the latest report.
"I don't know whether the samples sent to the labs were of my daughter or of someone else. Ever since the post-mortem was conducted every effort has been made to conceal the facts... Justice is being denied to us," he said.
Last month, the CBI attempted to exhume the bodies of the girls but their graves were under floodwaters and remain inaccessible to this day.
But India's Centre for DNA Fingerprinting and Diagnostics (CDFD) was able to examine the clothes and personal effects of the two girls and reported that it found no proof of sexual assault, a CBI spokesperson told BBC Hindi.
The CBI refused to provide any more details, but media reports quoting sources in the CDFD said "no male DNA had been found on the clothes and personal effects" of the girls and also "no female DNA was found on the samples taken from the male suspects".
The Indian Express reported that the laboratory analysed "items of clothing" and personal effects worn by the two victims as well as the clothes worn by the accused. It also said that blood samples and swabs from both the victims and the accused were examined.
The story of the hangings of two teenage cousins in a north Indian village is getting murkier with each passing day.
The initial reports said the lower-caste girls had been gang raped and hanged by young men from a slightly higher caste.
A post-mortem carried out on the girls by a team of three local doctors in Badaun said the girls had injuries "suggestive of rape".
Three men were arrested, along with two policemen, and remain in jail nearly three months after the crime.
But in recent weeks, reports being leaked by the investigators to Indian media have turned the story on its head.
Officials are now raising questions about the testimony of the victims' families - they say lie-detector tests done on the girls' families indicate "deception".
Questions have also been raised about the credibility of the main witness, a neighbour of the girls.
Some reports have said the murders may even be a case of honour killing.
All such reports have been vehemently denied by the family.
But the latest round of revelations from the CDFD has added a further twist to the tale
How federal investigators will reconcile the contradictory reports of the two major forensic investigations is as yet unclear.
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