An underpayment is usually an oversight, especially if this is a regular customer. The tone of the letter is not a slap on the wrist, but more of an effort to straighten out a misunderstanding.
1234, Main Street
Boston, MA 02123
<Recipient Address Goes Here>
We have received your payment of <$amount> on invoice number <invoice number>. Because <reason for underpayment>, you still show a balance owed of <$amount>.
<Method of handling.>
If you have any questions, please feel free to call us at <phone number>. Thank you for your prompt attention to this matter.
encl: <List of enclosed items goes here>