One source told us, "Everyone knows Michael is an animal activist. This would never happen on his set. There are dozens of witnesses who said that this didn’t happen."
Italian officials say otherwise -- prosecutors claim the pigeon was killed by a dolly while Michael was filming in Rome ... where it is illegal to harm or kill wild birds.
Authorities say someone from the set saw the whole thing, and took a photo before reporting it to law enforcement.
The allegation isn't that Michael himself harmed the bird, but because he was the director ... he's being held responsible for the incident. Michael reportedly tried to get the case thrown out several times, but prosecutors persisted.
According to The Wrap, who broke the story, Michael was given the option to pay a small fine to settle the entire case, but he declined, saying he simply wouldn't plead guilty to harming an animal.