We have Datacap Navigator application where we are using the start batch panel to get the account number from the user and user scans the document and submit the batch.Data gets transferred from client system to Datacap Server along with the start batch panel information such as account number

We have one ISD Application security review point where they have asked us to encrypt or mask the account number before transferring the data from client system to Datacap server to create the batch

How to do payload encryption over here?

Are you using HTTPS for both Navigator & Datacap wTM? I'd imagine if the entire environment is using HTTPS then communication would be inherently encrypted.