Files relating to the Kincora Boys' Home were destroyed between 2010 and 2015, the Northern Ireland Office has said.
Six files relating to the east Belfast boys' home that were created between 1981 and 1983 were disposed of.
The NIO confirmed the details in documents released under the Freedom of Information Act.
Lawyers acting for former Kincora resident Richard Kerr, who is suing police and a number of government bodies over claims he was abused at Kincora and other institutions, say there "must be an explanation" - or victims of abuse will continue to doubt the state.
Kincora Boys' Home was subject to investigation by the Historical Institutional Abuse Inquiry (HIA) between May and July 2016.
The HIA Inquiry was announced in 2010, and was legislated for the following year, with its terms agreed in 2012. The inquiry began its work in 2014.
In a statement KRW Law said: "It is unclear why the NIO would have files destroyed which would have been subject to scrutiny by the HIA."
According to information shared by the NIO in response to the FoI request, which was submitted by historian and biographer Andrew Lownie, three files relating to Kincora were destroyed between October and December 2010.
December 2010 was the month in which the HIA was announced following the publication of the Ryan Commission Report into historic institutional sexual abuse in the Irish Republic in 2009. It was the publication of the Ryan Report that prompted politicians at Stormont to announce the HIA.
Information shared in response to Mr Lownie's FoI request revealed files were also destroyed in August 2014, June 2015 and October 2015 as the HIA was conducting its investigations.
The files all relate to Kincora and include the Terry Report, a report compiled by Sir George Terry, Chief Constable of Sussex to Sir John Hermon, Chief Constable of the RUC.
The Terry Report was available to the HIA through RUC records.
Kevin Winters, senior partner at KRW Law, said: "There remain far too many questions around The Kincora Boys' Home. Our client Richard Kerr is seeking information by way of a civil action.
"It now transpires that documents - including the Terry Report - were destroyed by the British Government even as the HIA was being established and working.
"There must be an explanation for this. Otherwise, victims of abuse in Northern Ireland will continue to doubt the integrity of state agencies in confronting this particular aspect of the Legacy of the Past."
A UK Government spokesperson said: "The NIO handles its records in line with guidance from the National Archive.
"Records are only destroyed in line with this guidance, generally because they consist of publicly available information such as press cuttings, or they are duplicate copies of records available elsewhere in the public domain."
Last September this newspaper reported how 19 files on the Kincora scandal had been "closed" to the public.
In one case, the order remains in place until 2085 at the earliest. Around a dozen more of the files are closed - either fully or partially - until the mid-2060s and beyond.
Others which were scheduled to be declassified in recent years remain at least partly shut.
The department responsible for the records said they contained "sensitive personal data".
The Kincora scandal shocked Northern Ireland when it emerged in 1980.
At least 29 boys were sexually abused at the care home.
Three senior staff members - William McGrath, Joseph Mains and William Semple - were jailed in 1981 for the abuse. However, claims persist of a cover-up.