A former Army captain has described the Historical Institutional Abuse (HIA) inquiry findings on the former Kincora Boys' Home as "a mess".
The HIA report into child abuse at churches, charities and state institutions was published last month.
It detailed widespread mistreatment of young residents between 1922 and 1995.
However, former Army officer Colin Wallace has criticised its conclusions on Kincora, claiming they were "full of alternative facts".
Mr Wallace, who served in Northern Ireland between 1971 and 1974, has been a leading voice in claims about an alleged cover-up by intelligence services of sex abuse at the home.
The HIA report said Mr Wallace was offered the opportunity to assist the inquiry on two occasions but chose not to do so.
The former officer said this was because it did not have powers to compel evidential material and because it refused to provide a list of government files relevant to his evidence.
In a letter to the inquiry's solicitor, Mr Wallace accused the inquiry of "ignoring witnesses and evidence" and challenged its assertion that intelligence services did not cover up abuse.
"The inquiry went to extraordinary lengths to protect the RUC, MoD and intelligence services, who were using Kincora for intelligence gathering in the 1970s," he alleged.
Mr Wallace also claimed the HIA report "attempted to undermine" a memo he wrote in 1974 regarding information the Army received from the RUC about Kincora.
"The inquiry deliberately ignored forensic tests showing it to be genuine," he claimed.
In a statement, a HIA spokesperson said Mr Wallace "was requested to provide a witness statement answering questions the inquiry considered relevant and to provide copies of certain documents, but did not do so".
"The inquiry devoted 119 pages of its report to examining what Mr Wallace has said about Kincora in the past. The remaining documents relating to Kincora are due to be placed on the inquiry website in the near future.
"The inquiry does not intend to debate its findings with Mr Wallace and invites those interested in what he has to say to study the detail of the report and examine his correspondence with the inquiry and [its] conclusions about Mr Wallace's credibility."