The rumours have never been able to be confirmed. American Humane Association have tried though, without luck.
We have tried through humane people in Japan, and through another Japanese producer to determine if these rumors are true or not but everything has led to a dead end.1
Here are some of the deleted clips that were removed from the American release of the movie.
I linked to a specific time when a black bear attacks the little pug. In other clips the cat is being thrown off a cliff, and being attacked by a snake. Many of the scenes just looks too brutal, too real, to have been faked. Some can be done with well trained animals etc, but this is the concern many other have had about the movie as well.
Kent said her organization had a number of complaints from people who had seen the film and were concerned that it could not have been made without cruelty. [ 1 ]
[ 1 ] Gillespie, P. (April 15, 1990). "Cat Cruelty Claim Over Kids' Movie" The Sunday Mail