It has also emerged that witnesses in the north accused the armed forces of killing civilians in shell attacks.
The government says that defeated Tamil Tiger militants are to blame.
Former Ceylon Chamber of Commerce President Chandra Jayarathne said that after its victory celebrations last year the government should have undergone what he called a "process of atonement".
He said that he hoped the commission would lead to a "public expression of regret and apology on behalf of all the leaders and governments of the past, specifically to the war victims and to the nation at large".
Mr Jayarathne also said that, among other things, there was a perception that disappearances and arbitrary arrests were still continuing.
According to accounts emerging from the panel's visit to what was the Tamil Tigers' last stronghold earlier this week, a Tamil civilian who fled the war zone accused the navy of repeatedly shelling refugee boats as they crossed a lagoon to escape, even though they shouted that they were civilians.
Eight people were killed.
In separate testimony, a woman also described how her daughter and son-in-law were also killed by shells as they fled.
Witnesses accused the Tamil Tigers of violently trying to stop them from escaping.
The BBC was barred from the proceedings in the north - these accounts came from Tamil-language newspapers.