How to restrict Windows shared folders access to specific applications?

There are few shared folders in my company that are accessed by applications from different branches across the country for different transactions. Hence they are kept "open". During a recent PT exercise, this was reported as a finding. Though no write access is given, I understand that this is a security risk. The application owners claim that securing the shared folders would disrupt the normal running of the applications. I was wondering if there can be a secure set up so that only the designated applications can access these shares?