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Turmoil at the VA: New allegations against agency

The U.S. government agency that handles whistleblower claims wrote a letter to President Barack Obama on Monday detailing apparent contradictions within the Department of Veterans Affairs' own investigation of alleged misconduct, CNBC has learned

The U.S. Office of Special Counsel's letter, which was obtained by CNBC, focuses on the VA facility in Fort Collins, Colorado. The agency's findings are outlined in detail in the video here.

The VA, the second-largest federal government agency, is being investigated by several government watchdog agencies, including the Federal Bureau of Investigation.

A VA spokeswoman told CNBC in an email that issues related to Fort Collins remain under review "and we cannot speculate on what the findings may be." The spokeswoman noted that the VA protects whistleblowers from reprisal.

Read MoreVeterans Affairs Secretary Eric Shinseki resigns

The VA's 2015 budget exceeds $163 billion, and Congressional budget experts say new bills designed to help speed up veterans' access to health care could result in spending twice as much on veterans' health care over the next three years.

Exterior view of the Veterans Affairs Medical Center on May 8, 2014 in Phoenix, Arizona.
Getty Images
Exterior view of the Veterans Affairs Medical Center on May 8, 2014 in Phoenix, Arizona.

CNBC first uncovered fraud at the Department of Veterans Affairs 10 months ago, culminating in a documentary, "Death & Dishonor: Crisis at the VA," that was released last year.