You don’t say, but I’m guessing you’re using AxCrypt 1.x for this. Version 1.x is unsupported and unmaintained unfortunately. Even more unfortunately – AxCrypt 2.x does not yet support a command line client… You can integrate via source code inclusion, but it requires C#/.NET programming skills.
Allt his being said – there’s no fundamental reason why you could not use AxCrypt 1.x as you intend. You do have to handle the password in one way or another, typically passing it from an environment variable to the command line.