If you enter a payment deferral agreement with your lender it should not affect your credit score. The lender should be alerting all three credit bureaus that your loan is in deferment and that both parties have entered into an agreement. However, you may want to discuss this with your lender to ensure that they are properly following through with the reporting.
The timing of completing the agreement could also become a critical factor. If you know that you need a deferment you should make sure you give enough time for the deferment to be approved before the loan due date. If you do not allow enough time, you could potentially see a late payment on your credit report. If your credit is already fair or bad, any late payments can greatly affect your ability to get credit in the future. Even one late payment could drop a credit up to 100 points.