A young adult remained in the foster care setting at the centre of abuse allegations after the removal of the young woman known as Grace in 2009.
HSE Director General Tony O'Brien told RTÉ's This Week that the person was placed there privately.
In a statement this evening, the HSE said the young adult was removed in 2013, after her family was contacted by the HSE and the gardaí and told of "historical concerns in relation to the care of children in the home".
The foster care setting at which Grace was placed was the subject of allegations of sexual, physical and financial abuse stretching back to the early 1990s.
A decision was made by the then South Eastern Health Board not to place any further people with the home after 1995.
However, at a meeting of SEHB staff in 1996, a decision to remove Grace was overturned for reasons which were not recorded.
She remained in the home until 2009 when a local service provider took legal steps to place her in an alternative residential setting, following further concerns over injuries a carer believed were consistent with sexual assault.
More than 40 people passed through the care setting on health board placements between the early 1980s up to 2009, when Grace was removed.
However, Mr O'Brien has revealed that other people were placed there by private arrangement, one of whom remained after the removal of Grace in 2009.
He said "there were persons in that home over a long period of time in addition to Grace and the 44 people we have talked about, including some who were there privately, who remained after Grace".
The person, who remained in the home until 2013, had been originally placed with the foster family by private arrangement.
The HSE statement also pointed out that the family of the young adult had no complaints regarding the care she received.
Last week the HSE delivered an apology to Grace for failings in her care.
Last night the HSE revealed that it is no longer contesting a civil action being taken by Grace for failings in her care.
A garda investigation is also being pursued into the handling of Grace's care by staff in the then health board and the HSE.
The DPP recommended no prosecutions on foot of earlier investigations into the allegations of sexual abuse.
The HSE is also to appear in front of the Public Accounts Committee next week amid accusations of "lies" and "misrepresentations" by committee members over an apology to Grace the committee was told had been delivered in December.
However, a whistleblower who has made several protected disclosures to the PAC about Grace's case contested that this had taken place.
Witnesses to a meeting between Grace and HSE representatives made protected disclosures that no such apology was delivered.
The HSE was forced into a U-turn last night over its version of events.
It accepted no apology had been given.
Mr O'Brien said there had been "a breakdown in communication between the people who decided an apology should be made and the people who it was expected would be giving that apology".
He said he would be issuing a personal apology tomorrow.
Mr O’Brien said: "This is difficult to explain but it happens to be the truth, it would be different if there was some malign intent here, but there wasn't."
The HSE DG also said he felt an apology should have been delivered following the completion of a report on Grace's case in 2012.
He said: "If we were not on live radio there's a simple term I'd employ to explain what's happened here but it's not appropriate for national radio. This has been mishandled. This has not been good.
"I am concerned about the overall arrangements around the way in which written apologies were provided to all 44 people who received them and in particular that the events of the last few days will have added to the stress of all those who were at the centre of this issue.
“And for that reason, I myself will be sending further written correspondence with an unambiguous and sincere apology, in particular for what's happened in the last few days but also for the serious failings in care going back to 1983 so that there can be no doubt that a fulsome (sic) apology has been given," Mr O’Brien added.
