The Treasury watchdog, in its report, had said that the Internal Revenue Service (IRS) used "inappropriate criteria" to select conservative groups applying for nonprofit status for additional scrutiny.
"I have now had the opportunity to review the Treasury Department watchdog's report on its investigation of IRS personnel who improperly targeted conservative groups applying for tax-exempt status," Obama said in a statement.
Noting that the report's findings are "intolerable and inexcusable", the President asked his Treasury Secretary Jack Lew to take action in this regard.
The report said that the "inappropriate and changing criteria might have led to inconsistent treatment" of organisations applying for tax-exempt status.
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This led to "substantial delays in processing certain applications and allowed unnecessary information requests to be issued," the report said.
Obama said he has directed Lew to hold accountable the people who are responsible for these failures, and to make sure that each of the Inspector General's recommendations are implemented quickly.
"And as President, I intend to make sure our public servants live up to those standards every day," Obama added.
The watchdog report alleged that IRS employees "inappropriately" requested the political affiliations of members of the groups seeking nonprofit designation.
"Although the IRS has taken some action, it will need to do more so that the public has reasonable assurance that applications are processed without unreasonable delay in a fair and impartial manner in the future," the Inspector General wrote in the report.
"We believe the front-line career employees that made the decisions acted out of a desire for efficiency and not out of any political or partisan viewpoint," Joseph Grant, acting commissioner for the tax-exempt division, wrote in a letter included in the report.