Washington – A government watchdog has ordered the CIA and the Pentagon to re-investigate retaliation allegations brought by two intelligence employees who accused their agencies of major institutional failings. The action by the intelligence community inspector general is the first public indication that a new intelligence appeals system is underway. The panel was set up by President Barack Obama as an independent forum that can evaluate whether whistleblowers were improperly fired or otherwise punished for disclosures after their agencies rejected their claims. The cases, nonetheless, demonstrate that the whistleblower system continues to be beset with problems and bureaucratic delays despite being overhauled by Congress and the Obama administration. “Navigating the system as an intelligence employee is still very burdensome and overwhelming,” said Michael Helms, a former Army intelligence officer whose case is one of the two being kicked back. “A decade after I blew the whistle on inadequate care for military civilians, I’m still waiting for justice.” Obama pointed to the reforms when former NSA contractor Edward Snowden revealed he had decided to go to the media with classified documents about the spy agency’s data collection programs instead of relying on the whistleblower system. Snowden asserted that intelligence agencies couldn’t be trusted to look into serious malfeasance or to protect high-profile whistleblowers. The two cases are significant because they involve intelligence employees who say they were retaliated against even after they complained to Congress about what they described as significant problems at the CIA and the Defense Department. Dean Boyd, a CIA spokesman, declined to comment, as did Bridget Ann Serchak, a spokeswoman for the Pentagon inspector general’s office. The CIA case involves former contractor John Reidy, who asserts he was punished after warning of a “catastrophic failure” in the spy agency’s operations. “It was a recipe for disaster,” Reidy wrote in his appeal, which was redacted by intelligence officials. “We had a catastrophic failure on our hands that would ensnare a great many of our sources.” His lawyer, Kel McClanahan, said Reidy was in charge of identifying foreign sources and systems in the telecommunications and computer fields that would be of interest to US intelligence agencies. Reidy also was responsible for developing intelligence operations against those targets, his lawyer said. McClanahan said his client is not permitted to discuss the case in more detail even with him because the CIA says the information is classified. Reidy asserts that he first detected vulnerabilities in a CIA program in 2006, according to the appeal filing obtained by McClatchy. Signs of the problems included “anomalies in our operations and conflicting intelligence reporting that indicated several of our operations had been compromised,” he wrote, adding that he noticed “sources abruptly and without reason ceasing all communications with us.” He also alleged botched intelligence reporting. “Much of the reporting collected was titled ‘atmospherics’ that did not meet the standard of reportable intelligence (redacted),” he wrote. “Atmospherics generally consisted of scuttlebutt you could hear on the streets,” he wrote. “We still counted this reporting to bolster our metrics – because it was how productivity was determined.” At one point, Reidy said, he and others realized they had a “massive intelligence failure on our hands.” “I was told … upwards of 70 percent of our operations had been compromised,” he wrote. He said he reported the problems at a time when the “US communications infrastructure was under siege” by hackers. It’s unclear whether the vulnerabilities themselves involved hackers or not. The CIA excised the details from the appeal. “There is no doubt that what I have reported has been critical and embarrassing to (the) CIA,” Reidy wrote in his appeal. “I would have been able to provide more evidence to back up my appeal but (the) CIA holds all the cards.” Reidy asserted his supervisors and the CIA ignored the problems and punished him by removing him from his contract. “They did not want to admit the obvious because it was their funding, their platforms, their officers and their unwillingness to change course that (led) to future compromises,” he wrote. The other case involves Helms, the former Army intelligence officer, who blew the whistle on inadequate medical care for military civilians. Helms, who was based at Fort Knox in Kentucky, was initially refused treatment at Walter Reed Army Medical Center after he was wounded in Iraq as a gunner in 2004. Although he’d been hit by a roadside bomb while in an unprotected Humvee, the hospital initially wouldn’t admit him. The hospital told Helms he couldn’t be treated there because he wasn’t active-duty military but a civilian for the Army Intelligence and Security Command. After Helms complained to Congress, he was fired. The Pentagon inspector general’s office initially found the Army had retaliated against him. When the Army ignored the 2010 findings, Helms refiled his complaint. This time, the inspector general’s office reversed itself and dismissed his case. McClatchy learned from multiple US officials that senior officials at the Pentagon inspector general’s office have been accused of overturning the second finding although their own investigators had found in Helms’ favor. The intelligence community inspector general’s office reviewed the two cases after both men filed appeals. The office found that the CIA inspector general hadn’t demonstrated it had completed its investigation under Obama’s new requirements, known as Presidential Policy Directive 19. “In the matter relating to Mr. Reidy and the CIA, Mr. Reidy provided us with sufficient documentation required of him so that we could decide on his request for appeal,” said Andrea Williams, a spokeswoman for I. Charles McCullough III, the intelligence community inspector general. She added that her office did not receive that same documentation from the CIA, prompting McCullough to refer the case back to the agency. The CIA inspector general’s office has not responded, even though the case was referred late last year, said McClanahan, Reidy’s attorney. McClanahan said he has gotten the runaround from both the intelligence community inspector general and the CIA on whether he is cleared for access to discuss the case in detail with his client. “The IC IG told me I had access, but the CIA told me that I can’t accompany my client to an interview because it involved classified information,” he said. Making matters more difficult, Reidy was required to write his appeal without legal counsel in a secured facility and rushed out before he had time to edit it, McClanahan said. Helms, who says he can’t afford a lawyer, said he was told the Pentagon inspector general is now required to re-investigate his allegations or face the possibility that the intelligence community inspector general’s office will do it instead. After both agencies respond to the order, McCullough will determine whether to send the cases to the appeals panel or not. If sent there, the panel has a six-month deadline to decide the cases.