The order was issued by a division bench of the court while considering a case related to protecting the life of wild elephants.
Kochi unit DySP V S Uma will head the team. The Pocso court has set a deadline of three months to solve the case.
The court announced its decision while considering a petition filed by the mother of the girls.
The incident happened around Walayar toll plaza around 10.50pm on Thursday.
Crime Branch superintendent of police MJ Sojan had reportedly made an obnoxious remark about the girls.
The autobiography contains serious accusations against the chief minister’s office and police.
Vigilance had raided the checkpost and seized Rs 67,000 in bribes taken by the officials.
On sensing the presence of the team, the Assistant Motor Vehicle Inspector (AMVI) ran off to the nearby forest.
The charge-sheet also remarked that it had been very painful during the investigation to note the ordeal suffered by the two minor girls.
The CBI team which probed the the case has concluded that the girls committed suicide following serial sexual abuse.