One such program, ONESOURCE, comes from Thomson Reuters. Its latest version includes a Schedule UTP report, as well as the ability to track foreign currency adjustments. It also features process controls and is automated.

Until now, companies often used spreadsheets to account for uncertain tax positions. However, given the greater scrutiny -- both the IRS and SEC review this information -- companies have a greater need to ensure the accuracy and thoroughness of their calculations. "A manual spreadsheet may have been O.K. when there were less eyeballs reviewing it," says Joe Harpaz, senior vice president and general manager, corporate business of tax and accounting with Thomson Reuters.

Even companies that figure they have just two or three UTPs often find the calculations more involved than they initially assumed, says Claire Crossman, director of product management, corporate, the tax and accounting business of Thomson Reuters. That's because the positions often involve multiple years.

Or, the positions might have "tentacles to 20 or thirty areas," Harpaz says. An example would be a UTP that affects a company's tax liabilities in different states. For companies operating internationally, currency translations add to the complexity, as well.

What's more, the IRS' and SEC's disclosure rules differ, Crossman says. For the SEC, companies need to rank their tax exposures after considering the probability that the position will be sustained. The IRS, on the other hand, requires companies to ignore the probability and report the maximum exposure.