The transcripts and photos were part of Department of Justice files arising from investigations into the disgraced financier and his former girlfriend.
Newly released files show how Maria Farmer, who worked for Mr. Epstein in the 1990s, had urged the F.B.I. to investigate him. The case went nowhere for years.
A total of 16 photos were taken down at some point on Saturday from the website that the Justice Department created. One featured an open drawer containing other photos, including at least one of President Trump.