IRS regulations on timeliness of payments

We are being asked by our controller to provide an automated way to tax individuals on expenses that were requested after the 60 day IRS guideline.  We are exploring several options.  The easiest for my staff would be to provide a query to the payroll staff with the employees and their expense amounts by pay period.  It would run through payroll, and the employee would be taxed on the reimbursement.  We have also contemplated more complicated scenarios that don't require payroll staff to manually enter into the system.  My question -- is anyone following this IRS regulation?  if so, how