Speaking from Wellington, Dr Nitschke said this was the first time he had visited New Zealand in a private capacity for many years.
He said he was "surprised and shocked" at the level of scrutiny he was put through on arrival.
"Of course I have a copy of my own book on my Kindle and iPad and, yes, I have files for the current edition of the book on my laptop," he said. "None of these is intended for distribution, they are for personal use only. As author I would have thought it common sense to assume possession of them."
Dr Nitschke said the search would have been "comical had it not been so serious".
"To see New Zealand Customs officers searching through my Kindle library, amid my newspaper subscriptions and travel guidebooks, frantically trying to identify if my own 'objectionable' and banned book was there.
"On finding the book the Customs officers then told me that my 2011 edition 'was fine' and I was eventually allowed entry."
He said the search had created confusion about the classification of his book.
"I'm not sure what made the 2011 edition 'fine' or if, as author, I am allowed to own such a book, even if it is in digital format.
"What was so disturbing was the ruthlessness shown in the search for ideas that this country has decided are unpalatable and from which the community apparently needs protection."
Customs did not respond to questions last night.