An Internal Revenue Service inquiry into the Clinton Foundation is looking at questions over the well-connected charity's status as a registered nonprofit.

Rep. Marsha Blackburn, R-Tenn., noted that while the Clinton Foundation may be riddled with other problems, the issue of its tax exempt registration is what prompted the IRS to refer a congressional inquiry to an investigative division earlier this week.

"One of the things I think is so important on this is ... so many areas work on the not-for-profit sector, I want to make certain that there is clarity in this area of the code," Blackburn told the Washington Examiner. "I want to make sure that laws and rules are being abided by and that that sector has the ability to remain robust and healthy."

Blackburn led dozens of House Republicans in an effort to push the IRS, the Federal Trade Commission and the FBI to investigate aspects of the Clinton Foundation's operations that have raised red flags.

The Tennessee Republican said "sham charities" that have seemingly engaged in more obvious violations of tax law have been shut down while the Clinton Foundation has continued to thrive.

"You've got the conflicts of interest," Blackburn said of the Clinton Foundation. "They have a very small board, which leads to the good governance issues."

"Then you have the money trail issues," she added. "You also have their structure, and a year ago when we started looking at this, we were focused on the structure."

The IRS rejected a request from House Republicans to investigate the Clinton Foundation last summer with a simple form letter.

However, IRS Commissioner John Koskinen wrote in a letter to congressional Republicans on Monday that he had referred their inquiry to the Exempt Organizations Examinations Program for further review.

Beyond lingering questions over whether the Clinton Global Initiative has strayed too far from the mission it laid out in its original request for tax-exempt status, the charity has faced scrutiny of its donors.

The Clinton Foundation accepted millions of dollars from foreign governments and entities while Hillary Clinton served as secretary of state. Many of those organizations had business or preferred policies pending before her State Department, creating the conflicts of interest that have plagued Clinton on the campaign trail for more than a year.

The Clinton Global Initiative's unorthodox structure has also raised questions. Instead of funding charitable projects directly, the philanthropy operates by convening CEOs and other powerful figures at glitzy conferences.

Less than half of all Clinton Global Initiative projects have ever been completed.