They include the killings of politician-soldier Maj. Lucky Algama and STF chief SSP Upul Seneviratne.
The newspaper says details of these killings came to light in the course of CID investigations into the enforced disappearance of journalist Prageeth Ekneligoda.
The details contained in documents handed over, following a court order, by the military intelligence to the CID.
These murders had been committed with the use of the links the military intelligence had with top LTTE figures at the time.
It was the military intelligence that had planned the suicide bomb attack that claimed the life of Algama at a UNP rally in Ja-ela on 18 December 1999.
The confirmation comes in a report submitted to the Security Council by CID director at the time, DIG O.K. Hemachandra who had investigated the incident.
The then military intelligence chief, now a retired major general, is responsible for Algama’s killing, Hemachandra’s report charged.
The top LTTE figure who had supervised the suicide bomber has had close connections with this major general.
Premachandra had sought defence ministry permission to arrest him, but the investigation was covered up, saying the military could get discouraged.
The then government was led by president Chandrika Kumaratunga’s People’s Alliance.
Personal enmity
The CID has also revealed that personal enmity had led to the fatal claymore mine attack on SSP Seneviratne and his driver at Digana town in Kandy on 07 August 2006.
Three persons connected to the incident are being questioned at present.
At the time the peace accord was in force, he had been serving at Akkaraipattu, where he had close links with the Karuna faction and continued that connection even after Karuna abandoned the LTTE.
However, he had been murdered by using LTTE members owing to a dispute among the top military intelligence officers serving in the area.