The Senate voted Friday to confirm President Obama’s pick to head the beleaguered Internal Revenue Service, which has been under intense congressional scrutiny over its treatment of Tea Party groups seeking tax exempt status.

John Koskinen was confirmed in a 59-36 vote, below the 60-vote approval threshold that would have been required before Senate Democrats changed the chamber’s rules to prevent Republicans from continuing to block presidential nominees.

Obama immediately praised the confirmation, but Republicans mostly opposed it, in part because they are angry over the rules change and want a greater say in deciding who will next head the troubled tax agency.

In May, a Treasury Inspector General report found that the IRS had issued a “Be on the lookout” order for groups seeking tax exempt status with names that signaled a conservative bent, like “Tea Party” or “Patriot.”

Many of the Tea Party groups that applied for tax exempt status had their applications delayed ahead of the 2012 presidential election, prompting some to suspect the targeting was politically motivated.

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