The CID informed Colombo Fort magistrate’s court on August 10 that Karannagoda had been aware that the youths had been tortured at the Gunside camp in Trincomalee and killed subsequently.
The incident had been reported to the ex-commander through intelligence as well as through former minister Felix Perera.
It was also known to Commodore Udaya Keerthi, D.K.P. Dassanayake, Lt. Commander Ranasinghe, former intelligence director Guruge and other top Navy officials at the time.
Lt. Commander Hettiarachchi had committed the murders, but Karannagoda had complained to former DIG Anura Senanayake against Sampath Munasinghe over a personal dispute.
The TID got the information from the arrested Navy men and informed Karannagoda about the findings.
The court has been told that the CID investigator has come under death threats.
Navy sources say Travis Sinnaiah, who is tipped to succeed the incumbent Navy commander, is of the stand that the killers should be punished.