SEC Chairman Christopher Cox, in a letter to Comptroller General David Walker, pledged the agency intends to fix the problem, which was found by the Government Accounting Office and relates to the agency's reporting controls in fiscal 2007.

The problem, raised by the GAO in prior years, involves potential risks arising from the fact that some SEC computer systems aren't integrated or compatible, requiring manual processing or controls. Auditors must flag problems with internal controls if there is a chance they could affect financial reporting, even if they don't appear to have affected current results.

Cox said the SEC plans to introduce new software next year to address the integration problem and put an end to routine use of manual entries. The changes will affect the SEC's tracking of fines and return of illegal profits prior to disbursing them to investors harmed by wrongdoing. The SEC sought to collect more than $1.5 billion in fiscal 2007 and returned more than $2 billion to investors.

Earlier GAO audits had identified three material weaknesses at the SEC. Cox made eliminating such weaknesses a high priority and succeeded in fiscal 2006; even though the GAO found lingering problems, it said they weren't large enough to be material.

The latest audit findings were contained in the SEC's annual performance report released Friday. The report included fiscal 2007 statistics showing an increase in SEC enforcement actions, ending a three-year decline.