Internal Control - receipt of checks

A business unit receives a relatively large volume of checks each day (around a thousand checks a day on average).  In a recent audit, the auditors specified that checks need to be logged upon receipt. Because of the large volume involved, I'm wondering if anyone out there has experience with or is aware of an acceptable alternative (in regard to internal control) to literally manually logging each and every check every day in some sort of a check register.  Doing it that way would be very labor intensive and time consuming.  Thanks.