Obama said the Treasury Secretary had asked for and accepted the resignation of Miller, who was acting commissioner of the Internal Revenue Service (IRS).
"I have reviewed the Treasury Department watchdog's report and the misconduct that it uncovered is inexcusable. It is inexcusable and Americans are right to be angry about it and I am angry about it," Obama told reporters.
"I will not tolerate this kind of behaviour in any agency but especially in the IRS given the power that it has and the reach that it has in all of our lives.
"Given the controversy surrounding this audit it is important to institute new leadership that can help restore confidence going forward."
Requests for tax-exempt status by groups associated with the conservative Tea Party movement are said to have been subjected to "overly aggressive" reviews.
The US Justice Department has launched a criminal investigation.
Source: Euronews
