There was strong reaction last night from groups representing victims of abuse in residential institutions to the announcement of Ms Justice Laffoy's resignation.
Ms Christine Buckley of the Aislinn group said she was "devastated" at the news and Mr Colm O'Gorman of the One in Four group expressed "despair and disappointment".
However, Mr John Kelly of Irish Survivors Of Child Abuse (SOCA) welcomed it.
The Government is set to come under pressure from opposition parties on the issue today.
Fine Gael and Labour called on the Minister for Education, Mr Dempsey, to make a full and clear statement on the matter to clear up any doubts in people's minds as to the background of this resignation.
Ms Buckley said that on the three occasions she had been before Ms Justice Laffoy, she had found her to be "very fair and very impartial".
"She was listening very, very intently to what we had to say."
She said the religious orders and their legal representatives had hijacked the commission and strangled it, and that Mr Dempsey had allowed this happen.
Ms Buckley said the fact that Ms Justice Laffoy gave no reason for stepping down suggested that the major changes planned for the commission had to be the reason she decided not to go on.
"This Government seems to understand nothing about pain and justice. They allowed this happen in the hep C case and now it's us," she said.
Ms Buckley said there were no such difficulties in inquiries investigating the beef business or planning.
Aislinn, as well as representatives of Alliance, SOCA (UK), and the Right of Place survivor groups, had three meetings with the Minister and Department legal teams on the costs of the commission earlier this year.
They were to meet again on September 15th, but the Minister had pre-empted this with his announcement of another review of the commission on Monday.
According to Ms Buckley, that was done without consultation with survivor groups. They felt betrayed, she said, not least as the groups had been asked to keep silent until after the September 15th meeting.
Mr John Kelly of SOCA told The Irish Times that the commission "should have been scuppered a long time ago."
Its terms of reference had been drawn up by one of the defendants (the Department of Education) and was designed from the start to allow legal challenges, he said.
Mr Kelly said it was "a charade, and a facade". He called for an independent body from outside the State to oversee such an inquiry and said that if this was not done it would be necessary to go to the European Court.
Mr Colm O'Gorman said that as a society we had yet again collectively failed people abused in residential institutions.
In the four years since the Taoiseach's apology to such people, there had been few prosecutions and the commission set up to investigate was now dead in the water.
People who felt in 1999 there might be meaningful closure to what they had been through were now no further down the road towards that, he said.
Mr O'Gorman added there was "an urgent need for the Department of Education to publish all correspondence between the commission and the Department on the difficulties experienced [by the commission], given that the Department was one of the agencies under investigation.
"In the interests of compassion and justice this must happen without delay," he said. He believed the reasons for Ms Justice Laffoy's resignation must be published.
"We need to know what level of co-operation the commission received from the Department, the State, and the church authorities. It is depressing to imagine that we are at a point now where we may need an inquiry into an inquiry."
The Fine Gael education spokesperson, Ms Olwyn Enright, said the Minister for Education would have to make a full and clear statement on the matter so as to clear up any doubts in people's minds as to the background of this resignation.
The Labour Party's spokesperson on education, Ms Jan O'Sullivan, said the Minister must act swiftly to deal with the consequences of the decision.
The Minister's announcement of a review had "obviously created serious problems".
