Kathleen Sibelius said the payments resulted from "unintentional errors"
US President Barack Obama's second choice for health secretary has become the latest of his nominees to reveal tax payment problems.
Kansas Governor Kathleen Sebelius said she had recently corrected her tax returns and paid almost $8,000 (£5,560) in back-taxes for 2005-2007.
Ms Sebelius is due to testify at the US Senate on Thursday.
Tom Daschle, Mr Obama's first choice as health secretary, withdrew over questions about his taxes.
He stepped down after it emerged that he had failed to pay some $140,000 to the Internal Revenue Service.
Another nomination, that of Treasury Secretary Timothy Geithner, was criticised for his late payment of taxes, though he was eventually confirmed.
In a letter to the heads of the Senate Finance Committee, where Ms Sebelius is due to testify on Thursday as part of her confirmation process, she said the back-payments were the result of "unintentional errors".
They involved charity donations, a house sale, and business expenses and came to light in a review of their tax returns ordered ahead of the confirmation, she said.
She said that together with her husband she had paid $7,040 in additional tax and $878 in interest.
Max Baucus, the Democratic head of the committee expressed his support for Ms Sebelius.
"Congress is going to need a strong partner at the Department of Health and Human Services to achieve comprehensive health reform this year, and we have that partner in Governor Sebelius," he said in a statement.
Mr Obama has put affordable healthcare at the core of his domestic programme.