Offer a polite, appreciative response that helps clarify what is expected of you. Be sure you have a clear definition of your role from the outset to avoid misunderstandings later.
Send the acknowledgment letter within a couple of days of receiving the original letter, report, order, etc.
Include a short, sincere apology if the acknowledgment letter is delayed.
Since the reader may be dissatisfied or defensive, make this letter especially courteous. You may wish to apologize for any inconvenience, miscommunication, or problem, but emphasize that you are making restitution.
Be sincere—most people can sense when you aren't being honest.