Justice M.Venugopal gave the direction while hearing a petition by A Hithayatullah, the father of the victim, seeking a CB-CID probe into his son's death.
The boy's body was found floating in the Gurumilangudi Tank near Thondi in Ramanathapuram District.
The petitioner submitted that his son Mohammed Biaz was seen taken in a motorbike by three neighbours on May 2, 2016 and he did not return.
His son was found dead with severe injuries and contusions and it gave rise to suspicion that he had been tortured and murdered, the petitioner said.
He alleged that Thondi Police not only refused to accept the complaint initially, but to save the accused also took his signature in blank papers and forced him to accept that the boy had drowned himself in the tank.