I'm looking for a old movie with puppet rats that have to stop a real human from using a toxin on the rats but the man accidentally gets the toxic on him in the end but the puppet rats are told of a magical place or flower that will save them

I am pretty sure you are talking about "Blood Tea and Red String"

Sounds more like this:
A Rat's Tale (1997) - IMDb (http://www.imdb.com/title/tt0120220/)