International media are calling the series "mummy porn".
The trilogy has become popular throughout the world and became the fastest-selling paperback since records began.
Libraries and bookstores in New Zealand have struggled to cope with demand for the erotic novels, with more than 1000 readers on Auckland Libraries' waiting list.
There are now talks about the trilogy being played out on the big screen.
Whitcoulls book manager Joan Mackenzie said the list showed that there was huge diversity in the books Kiwis were reading.
"The Fifty Shades trilogy has taken the international reading world by storm and it appears New Zealanders are just as caught up in the hype," she said.
Other must-reads on the list include Suzanne Collins' popular Hunger Games series, which took second place, and the more traditional The Lord of the Rings by J.R.R. Tolkien, which rated third.
Further down on the list but still big favourites for Kiwis were Pride and Prejudice (4), the Harry Potter series (6), Song of Ice & Fire (8) -better known to many as HBO's Game of Thrones - The Pillars of the Earth (9) and The Hobbit (10).
For the first time, readers were asked to vote for their favourite author.
Jodi Picoult took out the top spot, J.K. Rowling second and the master of thrillers Lee Child came in third.
The most popular book since the Top 100 started in 1996 is The Lord of The Rings.
