In the letter, which was sent to senators and dated today, Sebelius wrote that she had made changes related to charitable contributions, business expenses and the sale of a home, according to the AP.
The wire service reports that she and her husband paid just over $7,000 in back taxes, along with $878 in interest, for the years 2005-2007.
Tom Daschle, the president's first HHS nominee, previously withdrew from consideration over tax issues, as did chief performance officer nominee Nancy Killefer.
Treasury Secretary Timothy Geithner, US Trade Representative Ron Kirk and Labor Secretary Hilda Solis, meanwhile, were confirmed despite issues related to their taxes.
UPDATE, 6:37 PM: CBS News has obtained Sebelius' letter to the Senate Finance Committee. She writes in it that she and her husband hired a Certified Public Accountant to review their returns after her nomination and that the CPA uncovered the errors, after which they amended their returns.
On the charitable contributions front, she writes that she could not locate three acknowledgment letters out of her 49 charitable contributions in excess of $250, and thus eliminated those three deductions.
She also writes that she had "insufficient documentation" for some of her tax dedications for business expenses, though because of the Alternative Minimum Tax they did not affect the amount owed. She also said she mistakenly paid off a home loan that included deductable mortgage interest.
Senator Max Baucus, who chairs the Finance Committee, released a letter backing Sebelius almost immediately after the tax issues came out.
"There is absolutely no doubt in my mind that Governor Sebelius has the political experience, determination, and bipartisan work ethic to get the job done with Congress this year," he said. "She's the right person for the job and I look forward to hearing from her at the Finance Committee's hearing on Thursday."