I'm thinking something like this: https://www.amazon.com/Akro-Mils-951.../dp/B00017IPLS

Put a piece of plywood inside, on the bottom, for strength. Drill some holes through the plywood and the box, and use big washers and bolts to attach the box on your bike's rear rack. Leave it permanently mounted on the rack. Maybe seal around the holes with Shoe Goo or similar to make it more waterproof.

Put the battery in it, maybe wrapped in a foam cushion to protect it from jarring. Close the box and put a padlock on the clasp.

The box could be removed from your rack, using tools, but if you do it right the tool user would need to get a wrench on a bolt head that is inside the locked box.

Note I know nothing about that toolbox I linked; I just picked it as an example of what I am talking about, it isn't a specific recommendation. I'd go to the hardware store and look for something like it that is sturdy, locking, and of a good size to fit the battery. There are both plastic and metal toolboxes out there. Plastic will be quieter and won't rust, but metal might give more security. The weak point in any such box is going to be the hinges so I'd pay close attention to those.