It means the documents will likely not be made public during the lifetime of the Duke - who is currently 63 years old, and would be 105 in 2065.
The revelation reportedly came as a result of a Freedom of Information (FOI) request made by royal biographer Andrew Lownie.
“Members of the Royal family are not subject to the Freedom of Information Act but I would hope with a new reign that only pertinent FOI exemptions such as national security, relations with another country, information given in confidence etc will be applied alongside data protection considerations,” Mr Lownie told the Telegraph.
“We are in the absurd position that Prince Harry can reveal the most intimate details of royal life from months ago for personal commercial gain and Royal households currently brief against each other, yet historians cannot look at files.
“It is extraordinary that files relating to Prince Andrew, the subject of my next biography, will be closed until 2065.”
Mr Lownie said “many questions remain” regarding the Duke’s former role as a trade envoy, and his associations with sex offender and billionaire financier Jeffrey Epstein.
Prince Andrew was the UK’s Special Representative for International Trade and Investment between 2001 and July 2011.
But the Prince was forced to step down from public duties in the wake of his disastrous Newsnight interview about his association with Epstein, who took his own life in jail earlier this year while facing sex trafficking charges.
In 2012, photos showed Prince Andrew walking through New York’s Central Park with Jeffrey Epstein. The Duke had reportedly been staying at Epstein’s New York mansion. The financier had been jailed two years earlier for soliciting prostitution from minors and served 13 months.
“There is also a strong public interest in knowing, for example, who is paying for [Prince Andrew’s] security now he is no longer a working royal,” Mr Lownie told the Telegraph.
It is understood that records transferred from the government to The National Archives at Kew are typically kept secret for 20 years, but
In a reply to Mr Lownie that was seen by the Telegraph, the Foreign Office reportedly said information relating to Prince Andrew would be kept from public view until 2065.
The Government response reportedly said: “Some information is being withheld under Section 37 (Communications with Her Majesty and honours), section 40 (Personal Information) and section 41 Information Provided in Confidence exemptions.”
The Foreign, Commonwealth, and Development Office (FCDO) has been approached by the Standard for a comment.