The commission headed by ex-high court judge T. Suntheralingam compiled the report in March 2006 to make recommendations to prevent HR violations during the war.
It has asked the government to withdraw emergency regulations in force at the time.
The report has condemned the use of the emergency laws and the PTA regulations to allow acceptance at courts of confessions made under duress.
The Suntheralingam commission, appointed to probe murders, rapes, harassment and illegal arrests, mostly in the northeast and the rest of the country, had managed to investigate only five incidents.
The state has not cooperated in providing the resources required and adequate time to investigate more than 30 complaints the commission had received from Trincomalee, Jaffna, Batticaloa, Ampara and Mannar.
Investigated only 5 incidents
The commission has investigated the abduction of TRO workers on 29 January 2006 at Welikanda and the subsequent disappearance of two of them, murder of five schoolboys in Trincomalee on 02 January 2006, rape and murder of a female at Pungudutivu, murder of the Kattankudy divisional secretary on 02 December 2005 and the death of five persons in a Judge T. Suntheralingam
bomb attack on 18 November 2005 at Akkarapattu mosque.
The TRO accuses the Karuna faction of having abducted its staff, while the commission has determined an armed group in Jaffna was responsible.
Noting reports that SP of the STF Kapila Jayasekara was behind the killing of the five schoolboys, the commission has expected justice in an investigation ordered by the then president Mahinda Rajapaksa.
It also said journalist Subramaniam Sugirdarajan, who exposed these killings, had been gunned down on 26 January 2006 at Trincomalee high security zone.
The commission is of the view that Ilayathambi Darshani had been raped and killed most probably by men from Pungudutivu Navy camp.
It said a paramilitary group operating in the east could have murdered Kattankudy divisional secretary Adam Lebbe Mohamed Faleel, and that unidentified group of groups might have bombed the Akkarapattu mosque to harm relations between Tamils and Muslims.
Other members of the commission were retired administrative officer M.C.M. Iqbal and head of the organization of war affected women Visaka Dharmadasa.
Attempts to contact the Human Rights Commission to ask about the delay in publicizing the report were unsuccessful.
No investigation has so far taken place into the continued use of emergency laws until five years after the commission handed over its report to the government, gagana.lk reports.