What is the process to remove the authority of MTDVAT to interact with HMRC ?

Once an authorisation has been issued, it shall remain in effect for a period of 18 months. The authorisation can't be revoked, instead you can "suspend" the account.

RoadMap to Suspend your Account
:  

 RoadMapHamburger menu → Client/Trader Manager → Select the client to whom you wish to suspend and click on View/Edit → Manage Assistant Administrator
→  Now, click on the  manager user option of the same client you wish to suspend → Suspend Account →  Enter the passcode with reason on why you choose to suspend the account  →  Click Confirm.

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