Seems the entire plot and character that Chris Elliot plays (character with a deformed left hand) was completely removed, including his name in the credit. Some scenes from "Scary Movie 1" was reinserted to "2" to increase the runtime as well.
It seems Japan has a real distaste for Chris Elliott unfortunately.
In seriousness,
This is a self-imposed censorship issue and not a government censorship issue. After WWII left many people maimed, burned, scarred, deformed, or handicapped physically, it became very taboo to physically handicapped people in negative or comical views in Japan.
Examples of Japanese films that came under scrutiny for such negative depictions:
http://en.wikipedia.org/wiki/Half_Human
http://en.wikipedia.org/wiki/Horrors_of_malformed_men
Again, it's what the distributor decided to do just so they could save themselves from a boycott from rights groups.