DUO with Office 365

We are using DUO 2FA to secure our users Exchange Online, but this has now caused us a problem with one of our applications.
We are using an online call logging system that accesses a user mailbox in Office 365 to send and import new emails, but since we have implemented DUO this has stopped working.
Does anyone know if there is any way round this?
I know this is fairly vague, but i am not sure what information you would need.