Do even better than that: have the government do random checks with drones, and if someone's found to be violating, seize their entire farm. Do make sure to include a provision to make sure they weren't non-compliant by accident (equipment failure not caused by illegal modification, or perhaps due to illegal action by manufacturer a la VW).

If you make the penalties for non-compliance devastatingly high, then very few people will risk it.

Also, companies found to be intentionally non-complaint like VW should simply be seized, not just fined. The executives should be tried criminally and imprisoned, and the rest of the company seized and sold.