Yes, you do. Regardless of who processes the amount claimed under a provider number, if there is any question about an amount to be recovered by Medicare the primary debtor will always be the doctor whose provider number is used to make the claim.
If you have a provider number and are rendering services you are a part of this system and you will be considered responsible for all services you claim. This applies regardless of the circumstances in which the services are rendered, whether they are bulk-billed or not, whether provided in a hospital or practice context, and regardless of the extent of your involvement in checking or submitting the claims to Medicare.
Even if your employer says they will indemnify you for billing errors, if your MBS billing practice is found to be inappropriate or incorrect (except when a shared debt determination is made by the Department of Health), you will be responsible for any penalties or repayments. Accordingly, it is in your interest to maintain tight control over your provider number and what is being billed under it.
If you do have to pay penalties or repayments to Medicare, reimbursement from your employer would be a separate matter between you and your employer. There is no guarantee that an employer would reimburse for any payments required to be made by Medicare, even if there is an agreement to indemnify.
One penalty for incorrect billing of item numbers can be a period where you are not allowed to bill those item numbers. It is unlikely any employer indemnity would include compensation to you for that time.
In many practices the administration of Medicare services is generally looked after by staff rather than by the doctor providing the service. This can be a convenient and efficient system that, when done properly, can assist to ensure you meet the item descriptors and are billing appropriately.
However, as the consequences rest with you, you must be satisfied that billings are being performed correctly. Ideally, you should sign off on all claims being made under your provider number before the claim is submitted, and you should retain a copy of all claims made.