Other than a few documents, most of the Vatican archives are kept secret from the public. What is the official explanation for this? As an outside observer, it seems like the secrecy might be to hide evidence for mistakes committed within the church, but I imagine the church would explain it differently.
"Secret" is probably about the worst possible translation I can think of for the original term. The "Archivio Segreto Vaticano" is the current term in Italian, as documented on the Archive's website. This translates the Latin "Archivium Secretum Vaticanum" (see for example the references here). Secretum in Latin, however, does not necessarily mean "secret". It can; but it can also mean "separate", "set apart", "private": see especially the II (β) entries in the Lewis & Short dictionary entry for the main verb form (secerno). The Archive itself, on its website, interprets segreto as meaning private, that is, personal to the Pope.
The documents themselves are not secret; they are indexed, with a publicly accessible index available in the Leo XIII index room, and documents in the index (organized by the man who was Pope at the time) are freely available for research by scholars, until (as it appears) the end of the papacy ending about 80 years ago; currently this allows access to documents issued in or before 1939, during the papacy of Pope Pius XI. (One can always speculate, of course, that there are deliberately un-indexed works present in the Archives which are indeed secret, in that there's no way for the public to request them; but I'm aware of no evidence that such might reasonably be the case.)
Pope St. John Paul II described the work of those staffing the Archivio Segreto as being fundamentally a public work, part of the overall work of the Vatican Library:
Your work is not confined to your efforts to preserve the books and manuscripts, the Acts of the Supreme Pontiffs and of the Offices of the Roman Curia, and to handing them on down the centuries, but above all it aims to make available to the Holy See and all the world's scholars the treasures of culture and art kept in the Archives and the Library. For this very reason it is also your duty to carry out attentive and detailed studies of these treasures, often with the help of other experts, so that they can be published with scholarly precision.
It is easy to understand the interest and care taken by my venerable Predecessors, especially in recent centuries, to create, promote and oversee the Apostolic Library, and later, as a fully-fledged branch of it, the Papal Archives. I am thinking of Nicholas V, Sixtus IV, Sixtus V, Paul V and many other Pontiffs, down to Leo XIII, who decided to open the Archives to scholarly research, and Pius XI, who was himself personally involved in this noble field of interest as Prefect of the Apostolic Library.
There is no "secrecy", then, involved in the "secret archives" of the Vatican; all the documents are available from roughly before any living person's lifetime (and many since their lifetime; for example, all the Vatican's documents on the Second Vatican Council and on the Vatican's "Information Office on Prisoners of War" from World War II have been made public). The word "secret" is merely an unfortunate mistranslation.