Agree with Wick, Cage aggression and defensive-ness often comes from fear (not always though! and sometimes people are well-meaning but just don’t know). I have been fostering a bunny (Bonnie) that was getting cage aggressive after being at the shelter a very long time, so I can tell you what has worked with her.
At the shelter she would box and lunge at your hands if you reached for her or reached into her cage, because she does not like to be picked up, and would have to be moved to exercise daily. So that took a toll on her over the years.
So when I brought her home, I made sure to have her pen all set up and ready for her before she arrived. Then for the first week I basically left her alone, except for to feed her. I’m in a studio apartment though, so she was exposed to us 24/7, we just didn’t try to interact with her. I didn’t open her pen at first, just to let her get settled (and she showed no interest in coming out anyway). I even tried to minimize litter box cleaning that first week (I cleaned it every 3 days instead of every 2), so her only interactions with me were me bringing her food. 🙂
Second week I started opening her pen, but she still didn’t want to come out. Third week I decided to open her pen at night while we were sleeping and things were nice and quiet (she hadn’t shown any destructive tendencies so I felt pretty confident she would be OK free-roaming with minimal supervision). I think that week she finally came out and would start zooming around the room around 3 am lol.
Then she started coming out while we were awake. I would sit on the floor and basically ignore her. Oh, and I hand fed her, A LOT. Especially high-reward things, like pellets and treat. Once she started relaxing near me, I was able to sneak in a few nose rubs.
Since then she has become more and more social, and now loves getting pets, and does not show any aggression at all if you reach for her. She’s been with us a few months now. She honestly seems like an entirely different bunny!
I do pick her up for nail trims and occasional deep grooming, but she is even better with that since she isn’t getting picked up all the time.
So I would say with your new bun, make sure he has a good pen or condo set up that he can feel safe in. When he is in his space, don’t try to pet him, but do offer a treat and feed him. Make sure he can come out to exercise on his own, and that you don’t need to carry him or pick him up except when necessary. When he comes out and is relaxed around you, you can eventually try to pet him, but don’t try to force affection on him. He will come to you when he’s ready. 🙂
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.