Kenneth Johnson, the acting finance chief of the Securities and Exchange Commission for much of the past year, has been named CFO of the agency.

“My two top priorities will be to ensure strong internal controls and to manage responsibly the agency’s growing budget,” he told CFO in an e-mail. “Not only because they’re required, but because they are key to effective financial management.”

Johnson said he learned “the importance of internal controls” first as a commerce analyst at the Congressional Budget Office, and subsequently as the chief management analyst and then acting CFO at the SEC. He joined the agency in 2003 as a management analyst in the Office of the Executive Director and became chief management analyst in 2006.

Part of Johnson’s job as management analyst was to oversee the development of the SEC’s long-range strategic plan that would guide agency policy through fiscal 2015. One of the plan’s targets is to achieve “an unqualified audit opinion on SEC financial statements and no material weakness or non-conformance.”

In that light, it’s easy to see why ensuring strong internal controls is a top priority for the new finance chief. In its audit opinion of the SEC’s financial statements for fiscal years 2009 and 2008, the U.S. Government Accountability Office found that the agency “did not have effective internal control over financial reporting as of September 30, 2009.”

During the audit, the GAO identified “six significant deficiencies that collectively represent a material weakness in SEC’s internal control over financial reporting.” The flaws included the agency’s internal control over information security, financial reporting, and maintaining fund balances with the U.S. Treasury. The agency also fell short in its controls over registrant deposits, budgetary resources, and risk assessment and monitoring processes.

As a management analyst, Johnson, 37, advised the SEC on all aspects of the budget process, developed strategy initiatives, and responded to inquiries from Congress and the Office of Management and Budget about the agency’s budget and financial operations.

As CFO, Johnson will lead the SEC’s Office of Financial Management, which handles budget, finance, and accounting operations for the agency. “I’m delighted that Ken has agreed to take on this role at the SEC,” commission chairman Mary Schapiro said in a press release on Friday. “His deep experience in the financial arena will be incredibly valuable as we grow as an agency.”

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