How to permanently disable 'Apple can't check app for malicious software' warning for known safe apps?

You cannot. Apple is only going to keep tightening up security & making it more annoying to use anything not provided by the App Store or a known & registered Apple developer. If you've been using macOS for any length of time, you should have already seen the signs of how Apple's security has been changing in all manner.....even with the installation of apps.

Your only option is to become a recognized Apple developer so that you can sign your own apps which will allow them to be installed on macOS without any problems (you will need to keep up on all the changes Apple makes for developers so your apps always comply with any new changes to macOS security).

Become a member - Apple Developer Program

Re-ask this in the code-signing community:

https://developer.apple.com/forums/topihttps://developer.apple.com/forums/thread/707080

You’ll also want to provide a little more detail, such as the particular file organizations of the files triggering this error — shell scripts, app bundles, or something else entirely — involved.

For some background on code signing, start here:

Code Signing Resources | Apple Developer Forums

You might be able to use an ad-hoc signature here, but maybe these programs — shell scripts? — cannot be signed?

You probably need to re-work your current (ad hoc) app distribution model into something a little more structured too, whether acquiring developer IDs and notarizing these apps with notarytool, or maybe obtaining an enterprise certificate. This all given the ever-more-restrictive path Apple is on now.

You can also ask Apple Developer Support directly: Support - Apple Developer

Jerbee02 wrote:

How can the "Apple can’t check app for malicious software" error be permanently disabled? Individual exceptions for specific programs can be made by going to Settings > Privacy > Security, but as part of my job, I install a large volume of "unknown" developer apps. These are not known by Apple, but known by our team, and are safe.

Where are you getting these apps? How do you know they are safe?

Having to manually approve each time has been time consuming and burdensome, and I cannot find any way to disable this security feature. Help?

This is a bit of an ethical dilemma. Should I refuse to answer based on my disbelief of your first statement? Or should I answer out of concern that you'll find the answer somewhere else and then stop asking questions here and go to some other source where you're likely to get into deep trouble?

Logically, if you aren't able to discover the multiple methods available to disable this alert, or even to identify the name of the security subsystem that generates them, then you would probably be putting yourself at risk by disabling it.