First Minister Jack McConnell has made a "sincere and full" apology to the victims of abuse in children's homes.
Jack McConnell made a full apology to victims
He apologised on behalf of the people of Scotland, rather than the executive, to protect ministers from legal action.
Mr McConnell told Holyrood that the abuse was "deplorable, unacceptable and inexcusable" - but stopped short of agreeing to a full public inquiry.
That demand had been made by alleged victim Christopher Daly, who said the apology was "a huge leap forward".
Education Minister Peter Peacock later set out proposals to offer more effective support to victims.
He said an independent expert would be appointed to investigate the regulations in place during the years of the alleged abuse, and the way they were monitored.
The debate was promoted by a petition submitted in August 2002 by Mr Daly, who claims he was regularly beaten by nuns at Nazareth House in Aberdeen in the 1970s.
He had urged the Scottish Executive to follow the Republic of Ireland's lead and offer a public apology and compensation to victims.
Mr Daly said: "My initial reaction was that his statement was very heartfelt and it was long overdue but an apology is a huge leap forward from where we were six months ago.
"I hope all the institutions involved will do the same and apologise unconditionally."
Mr Peacock had ruled out a public inquiry in September and said he could not apologise because a number of court cases were pending.
Chris Daly: "Huge leap forward"
However, MSPs took a stand against the executive after more than 1,000 people came forward with allegations of physical or mental abuse in Scotland's homes.
The public petitions committee decided that the allegations of abuse over the last 60 years in homes run by the state, children's charities and religious orders warranted a debate in parliament.
In a statement on Wednesday, Mr McConnell said it was clear that children had suffered physical, emotional and sexual abuse in the homes where they had hoped to find love, care and protection.
He said: "Those children, adults today, deserve full recognition by us of what happened to them then.
'Abuse and neglect'
"They should not have been abused. They were badly wronged.
"Such abuse of vulnerable young people whenever or wherever it took place is deplorable, unacceptable and inexcusable."
The first minister continued: "That is why I offer a sincere and full apology, on behalf of the people of Scotland, to those who were subject to such abuse and neglect."
To applause, he said: "They did not receive the level of love, care and support that they deserved and they have coped with that burden all of their lives."
Mr McConnell said he was unable to take his comments further because he did not
want to "cut across" litigation currently before the courts.
He told MSPs: "Those proceedings will establish, in accordance with the law, where responsibility lies and what should happen as a result."
The statement received an "unreserved" welcome from the Scottish National Party's Holyrood leader, Nicola Sturgeon.
She said: "The extent of the emotional, physical and sexual abuse suffered over the years by too many children in care homes is absolutely horrific.
"It is right and essential that that horror is acknowledged."
Tory deputy leader Annabel Goldie paid tribute to the courage of those who had come forward to tell of "these dreadful events".
She said: "It is important that this parliament sends out a clear message to the victims of such harrowing experiences - that we stand with you and that you are not diminished, stained or set about by what happened to you."
Survivors of abuse
Ms Goldie said an independent inquiry should be set up to uncover the problems of the past and evaluate the effectiveness of the measures put in place over the last 10 years.
Scottish Liberal Democrat leader Jim Wallace said: "We have come to this parliament to apologise and show our respect for the survivors of abuse.
"Words themselves cannot remove the pain, expunge the memories or wipe away the blemish."
The Greens, the Scottish Socialists and the parliament's independent MSPs also backed the apology.
MSPs agreed unanimously to take note of Mr Daly's petition in a vote at the end of the day in parliament.