The rules have applied to German cinemas showing adult films since 2002, but they are now being extended to cover books available on the internet.
It follows a complaint that a sexually explicit e-book titled Schlauchgeluste was too easy for children to obtain.
One book industry blogger said the decision, taken by the regulator Youth Protection Authority, was "just nuts".
The German Publishers and Booksellers Association confirmed that retailers were now considering ways to enforce the rules.
It has been suggested that they will have to start tracking the titles that count as "youth endangering" under German law, isolate them in a specific section and make them invisible using filtering software.
But Jessica Sanger, from the legal team at the German Publishers and Booksellers Association, said: "A time lock doesn't seem to make a lot of sense to us as kids can find ways to circumvent that.
"A system that requires proof of age is harder to circumvent and that is the way we see things going."
Booksellers face fines of 50,000 euros (Â£35,000) if they do not comply with the rules.
Digital media blogger Nate Hoffelder said it did not make sense to apply the legislation to e-books.
"Given the prevalence of adult content on websites outside of Germany, trying to control access on sites in Germany  is just nuts," he wrote on his Inks, Bits and Pixels blog.
"Even King Canute knew that he could not hold back the tide, but apparently German regulators lack that level of common sense."
The decision to change the rules was sparked by a transgender memoir called Schlauchgeluste (Pantyhose Cravings), which became the subject of legal action over its easy availability in a bookseller's database.
Germans will be able to buy adult-themed e-books only between the hours of 22:00 and 06:00, under new rules.