Create an active channel for complaints.
Employees need more than just a suggestion box to discuss their complaints. Companies should make their employees aware that they have a phone line, e-mail or a point person or office to report their grievances. Ensure these channels are "active" - meaning a response from someone handling the problem received their message and are in the process of resolving it.
Choose the right person or department to handle complaints.
Employ and/or appoint a person/s with a legal and human resources background. They will be handling problems with a legal nature and they should know how to best approach and deal with it. The person or team in charge of this task should also have little to no personal relationship to the employees to ensure fair and unbiased actions.
Instead of a complaint cascading down the office gossip vine and making the situation appear worse than it is, management should be transparent that about payroll complaints especially if there's more than one similar case. Companies should also be transparent how they are handling the problem and when it will be resolved. Keep the employee/s concerned on any updates about the matter. If there is lack of action and transparency on your part, the employee may blog or post about it which can become viral or hire the services of a lawyer which becomes a heavier charge for the company to take upon.
Don't terminate the employee.
Terminate the problem instead. If you think firing a disgruntled employee saves you the time and effort of solving their payroll issues, think again. Terminated employees on a baseless or unfair reason can back at you with a vengeance. Prevent lawsuits by immediately solving payroll complaints and if there are unforeseen delays in doing so, be honest to the employee about it.
Investigate the issue thoroughly.
Find out how inconsistencies or discrepancies reflected in the employees' payroll. Discover the faults in the payroll system and identify if someone in the accounting and finance department made an honest mistake. Ensure the same mistake won't happen again and settle on a plan of action to remedy the situation.