The commission's proposal to have a single team of barristers representing all survivors of abuse has been strongly criticised by some of the groups representing victims.
There was isolated heckling from the audience of up to 400 throughout Ms Justice Laffoy's opening address yesterday. However, it reached a height when she asked survivors to consider the proposal on legal representation "in the spirit in which it is made, as being, in the commission's belief, the best choice for the survivors".
Her appeal was greeted with cries of "No way, judge" from some members of the audience.
Explaining the reaction afterwards, Ms Josephine Baker, director of the Organisation for Recovery from Institutional Abuse, said survivors were "dismayed" that they could not be represented by the solicitors and barristers already familiar with their cases. "We don't want to have to go through our stories again with a bunch of strangers."
Mr Gerard Kelly (43), a survivor of abuse in three institutions, said he would boycott the inquiry unless he could have his own legal team.
"This is a farce. All of the tribunals at the moment are allowed to have their own people. Why shouldn't we?"
Ms Justice Laffoy conceded it might not be possible to agree on the composition of a single legal team, in which case, she said, it should be chosen by an independent person such as the chairman of the Bar Council or the president of the Law Society.
Such an arrangement, she said, would ensure survivors would be represented by lawyers with a broad knowledge of all of the facts and issues arising at the private hearings of the commission's investigative committee. The proposal would also result in more effective and expeditiously conducted hearings, she said.
Backing the proposal, Ms Christine Buckley, of the Organisation for Healing of Victims of Institutional Abuse, said she believed the "healthiest thing" was to select a legal team which had not been involved in any particular cases up to now. "It gives it a very objective, honest view."
She added that she was "absolutely thrilled" that a public inquiry was finally being established. "I would say this is justice for many people. From a therapeutic point of view, it is serving victims very well."