Steven Miller, who had been acting IRS commissioner, denied there was any effort at partisanship during a hearing with the House Ways and Means Committee.
"I want to apologize on behalf of the Internal Revenue Service for the mistakes that we made and the poor service we provided," Miller said. "The affected organizations and the American public deserve better. Partisanship and even the perception of partisanship have no place at the Internal Revenue Service."
He said it was a misguided effort to handle a flood of applications, not political bias.
Miller and another top IRS official are stepping down, but the chairman of the committee said that would not be enough.
"The reality is this is not a personnel problem. This is a problem of the IRS being too large, too powerful, too intrusive and too abusive of honest, hardworking taxpayers," said Rep. Dave Camp, R-Mich.
It was the first hearing into the scandal that forced the Obama administration to again be on the defensive. The president has said he didn't know about the targeting until last Friday.
Republicans are trying to link the Obama administration to the scandal. But Democrats said repeatedly that the IRS commissioner in charge when the inappropriate actions took place was appointed by President George W. Bush.
The Associated Press contributed to this report.
