There can be a number of reasons why batches don't automatically process correctly, error, late refund, Incorrect/Unbalanced re-processing failed, etc., and in some cases they will need manual intervention. Below are instructions on how to do this, with screenshots further below.


Before starting, you will need to know:

  • Medilink Batch Number(s). (Note: the Medicare Claim Id is *different* to the Medilink Batch Number since 2022 Web Services changes.)
  • Processing Report(s) (unless a batch was paid in full, in which case, you just need to know that amount).
  • In some cases you will need to manually obtain these reports from Medicare, as Medilink is only able to get the last report for a batch via electronic means.


1. Go in to the Medicare Online Control Centre screen. Type in the batch number in the field provided.


2. Click Revert To Unpaid, and when prompted to delete all previous receipts and adjustments, most practices prefer to say YES (cleaner history).


3. Click Manually Pay Batch. If you are on an older version of Medilink, you may have to use the Office Menu -> Medicare Payments/DVA Payments.


4. Type in the total amount paid for the batch in the Cheque Value field, and tick Payment by EFT, then click OK. Ignore the warning about manually processing an online batch. Note, if you are manually late refunding Medicare/DVA (i.e. they paid but you're paying it back), you'll need to manually calculate the amount; it's the total they originally paid less the amount refunded.


5. Find and click on the patients and items that need manual processing. Type in the amount that was actually paid for that service (which may be zero if it was fully rejected or is being late refunded), then click the Pay button underneath. Repeat for any other patients/items that need changing. Note, you can leave the lines that were paid in full as is (you don't have to change them at all). When you have applied all of the processing, and the amount being paid for the batch matches the amount you indicated in step 4, the OK button should light up - click it.