Without revealing the specifics, the sources said that on some questions, there were "deviations" during the tests. Sharing any further details may hamper the investigation, they added.
Read: Badaun victims' fathers to undergo lie-detector test
The two girls, cousins aged 14 and 15 years, went missing from their house on the night of May 27 and their bodies were found hanging from a mango tree in the village in the Ushait area on May 28. Post-mortem reports of the two girls confirmed that they were raped before murder.
The five accused - brothers Pappu Yadav, Awadhesh Yadav and Urvesh Yadav and constables Chhatrapal Yadav and Sarvesh Yadav - have been arrested in connection with the case which has sparked nation-wide outrage and led to concerns over the law and order situation in Uttar Pradesh.
A Central Forensic Science Laboratory team carried out the polygraph test here on the accused.
The CBI sources, without revealing the details of the process, said that several questions related to the crime and their alleged involvement in it were put to the accused during the tests.