The President was addressing the Golden Jubilee of the Conference of Religious of Ireland (CORI) at the weekend in Malahide, Co Dublin.
"These 50 years have been a process of adaptation sometimes to welcome changes but often to unwelcome change," Mrs McAleese said.
"The world metamorphosed from an era of deference to an era of declamation."
In a remarkably hard-hitting speech, Mrs McAleese compared the legacy of paedophile clerics for the religious orders to the financial burden of Nama on taxpayers.
"The millstone of the Ryan and Murphy reports will be carried for a long time on the way ahead, just as the millstone of the massive fiscal mistakes will similarly have to be carried for some time. There is a long road ahead to redemption on both accounts."
In the 50-year history of CORI, the story, as the Ryan and Murphy reports revealed, also had "some dreadful chapters", said Mrs McAleese.
Clericalism
The President referred to "the rigid hierarchicalism and powerful clericalism" which characterised the Irish church before the Second Vatican Council in the early 1960s.
This culture, she said, "created vacuums of vulnerability and unaccountability where children in particular suffered outrageously".
But Mrs McAleese was applauded by the mainly elderly religious when she highlighted the contribution made by CORI to Irish society and of their determination to restore healing.
Referring to the conference theme of 'Walking the Way', Mrs McAleese said this signalled that the religious were "here to prepare for the journey, as volunteers who are not paralysed by the scale of the difficulties but who have a profound belief that there can be healing, there can be renewal, there can be change for the better. You are here because you have or want to have hope," she added.
Mrs McAleese said that the orders represented "an unequalled and unrivalled investment in Ireland".
She spoke of the contribution of religious to education, health and social welfare, and of the physical, pastoral and spiritual enrichment of the Irish people.
"The story has many good, even great chapters," she continued. "You and your predecessors created and sustained, and on a not-for-profit-basis, much of the founding infrastructure of today's education and healthcare systems and outreaches to the poor and marginalised.
"Through the important impact you have on each individual, they are changed, families are changed, our communities and our country are changed."
CORI, Mrs McAleese added, was "probably best known for its championing of a fair and just society and for its advocacy on behalf of people whose lives are blighted by poverty and social exclusion".
Mrs McAleese congratulated the religious congregations for driving forward the agenda of Vatican II within each congregation at a pace well ahead of other sectors. She praised their role in aiding "the growth and development of modern Ireland".
She added that "green shoots" already nurtured by the religious orders had begun to alter the landscape.
"Today there are exciting new trusts and broad-based partnerships involving individual and collectives of congregations along with the laity and civic society spelling a collaborative and inclusive future which would have been unthinkable 50 years ago," she said, "but which honours both the letter and spirit of the Vatican Council."
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