The author was apparently very disappointed in this treatment because of the way the screenplay ended. he specifically said that the portion left out of the movie is what the book's name comes from and the themes covered are the only thing that makes the first part coherent.
Kathleen Kennedy was involved in making an adaptation of the book and completing it in its entirety (probably to the satisfaction of the author) but the project fell through and it looks like we won't be getting any new adaptations soon.
Hey, yeah, that's right. Michael Ende wrote the book and demanded his name wasn't in the movie credits.. Still, I love the movie and the book just the same :)
I have yet to read the book but maybe some day I will get around to it!