As it continues to police public company financial reporting, the Securities and Exchange Commission has demonstrated once again that it can’t get effective control over its own financial reporting.

In its latest report on SEC financial statements, the U.S. Government Accountability Office said the SEC’s 2008 and 2009 financial statements are fairly stated, and the government auditor found no problems with SEC’s compliance with laws and regulations based on the testing performed. However, GAO says the SEC ended its fiscal year on Sept. 30 with ineffective internal control over financial reporting, a now recurring theme since the SEC was first required in 2002 to submit audited financial statements to Congress and the Office of Management and Budget.

“In connection with our prior audits, the GAO has made numerous recommendations to the SEC to address the internal control issues that continued to persist during fiscal year 2009,” the GAO wrote in its report. The deficiencies that most troubled the government auditor were problems with information security, financial reporting processes, fund balance with the U.S. Treasury, registrant deposits, budgetary resources, and risk assessment and monitoring processes.

The deficiencies add up to a material weakness, the GAO said, giving good reason to wonder whether data processed by the SEC’s systems are reliable and adequately protected. The problems also force the SEC to rely on “extensive compensating manual procedures” and result in errors and unsupported entries in the general ledger.

The GAO says it noted in last year’s report that the SEC relies too heavily on processes and systems that are not designed to give accurate, complete, reliable information. This year, the GAO adds that it appears the SEC was not able to commit the amount of effort and resources necessary to compensate for its deficient systems and processes.

“These deficiencies are likely to continue to exist until the SEC’s general ledger system is either significantly enhanced or replaced, key accounting activity is fully integrated with the general ledger at the transaction level, information security controls are strengthened, and appropriate resources are dedicated to maintaining effective internal controls,” the GAO wrote.

In a response attached to the report, SEC Chairman Mary Schapiro says the SEC will make resolution of the problems “a priority of the very highest order.” She notes some of the issues underlying the deficiencies “have been building and accumulating for years. While some of them can—and will—be addressed quickly, others will take more time to solve. But our resolve to diligently correct all of these problems is strong.”

Even the GAO is quick to point out that the SEC’s already strained credibility is getting stretched with these persistent unflattering audit outcomes. “Successfully addressing these issues is critical to maintaining the SEC’s credibility given its important role in the financial reporting process of registrants, and is vital to achieving the SEC’s stated vision to be the standard against which federal agencies are measured,” said the GAO.