Answer:
Regulation E and the federal Electronic Fund Transfer Act afford protections only to individual consumers. Any protection from fraudulent ACH transactions in your institution's accounts would be addressed in your bank's deposit account contract and/or state laws.
By far the best protection against such fraud is careful attention to safe computing practices, use of dual control features and other practices your bank should encourage, and careful attention to daily transactions in the account.
First published on BankersOnline.com 1/24/11