CBI sources said they will soon be filing its final report recommending closure of the case before the court where it will give all its findings.
The agency is also likely to recommend action against Uttar Pradesh police officers for "erroneous" probe.
In Badaun, the families of the girls - who were cousins - rejected the CBI conclusion. They sought the intervention of Prime Minister Narendra Modi to ensure an independent and fair probe.
"How is it possible that the girls could have committed suicide together from a tall tree...I appeal to Modiji to ensure that we get justice," he said.
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The girls, who were 14 and 15, were found hanging from a mango tree near their village on May 28, a day after they were reported missing.
CBI sources said the agency will put forth details of alleged destruction of evidence against three family members and a relative Nazru in its report but it will be left to the court to take a final view.
"The medical report from multi-agency medical board, corroborated by team of doctors which conducted first post-mortem during their examination, conclusively says that girls had committed suicide," a senior CBI official said.
The report received from CDFD showed that there was no presence of male DNA on the clothes of the girls and there was no presence of female DNA on the clothes or body of prime suspect in the case thus ruling out any sign of violence or sexual assault, the sources said.
They claimed the girls committed suicide as the affair of elder one with a local boy was exposed while younger one who was in the know and also kept vigil while the couple was meeting too felt stigmatised.