Two senior intelligence analysts at U.S. Central Command say the military has forced them out of their jobs because of their skeptical reporting on U.S.-backed rebel groups in Syria, three sources with knowledge of their claim told The Daily Beast. It’s the first known instance of possible reprisals against CENTCOM personnel after analysts accused their bosses of manipulating intelligence reports about the U.S.-led campaign against ISIS in order to paint a rosier picture of progress in the war.

One of the analysts alleging reprisals is the top analyst in charge of Syria issues at CENTCOM. He and a colleague doubted rebels’ capabilities and their commitment to U.S. objectives in the region. The analysts have been effectively sidelined from their positions and will no longer be working at CENTCOM, according to two individuals familiar with the dispute, and who spoke on condition of anonymity.

The analysts’ skeptical views put them at odds with military brass, who last year had predicted that a so-called moderate opposition would make up a 15,000-man ground force to take on ISIS in its self-declared caliphate. An initial $500 million program to train and arm those fighters failed spectacularly. And until the very end, Pentagon leaders claimed the operation was more or less on track. Lawmakers called the plan a “joke” when Gen. Lloyd Austin, the CENTCOM commander, finally testified last September that there were just “four or five” American-trained fighters in Syria.

Earlier allegations from CENTCOM, the military command responsible for overseeing the Middle East, had focused on leaders there fudging intelligence reports about U.S. efforts to attack ISIS and undermine its financing operations. That analysts are now raising red flags around reporting on Syrian rebel groups suggests that, at least from the analysts’ perspective, there is a broader systemic problem than was previously known.

The Pentagon inspector general and a congressional task force are investigating allegations of doctored intelligence reports about ISIS.

The working environment at CENTCOM has been described as “toxic” and “hostile.” As The Daily Beast previously reported, more than 50 CENTCOM analysts have said that senior officials gave more scrutiny and pushback on reports that suggested U.S. efforts to destroy ISIS weren’t progressing. Analysis that took a more optimistic view of the war effort got comparatively less attention from higher-ups.

In a separate development, the head of Iraq analysis at CENTCOM, Gregory Hooker, is being reassigned to a position in the United Kingdom, three sources knowledgeable of the transfer told The Daily Beast. Hooker was identified last year by The New York Times as leading the group of analysts that raised objections about the ISIS reports.

There was no evidence that Hooker’s reassignment was a retaliatory move by his superiors; rather some suggested he had requested the change.

But for the analysts who have accused their bosses of improper behavior, the climate has become anxious, particularly as now some fear for their jobs.

“[They] are scared all the time,” one official told The Daily Beast.

The Syria analysts spoke out after Austin directed his subordinates last year not to retaliate against anyone who voiced concerns about political influence or bias being brought to bear on intelligence analysis, said one individual knowledgeable of their complaints. More than 1,000 analysts work at CENTCOM headquarters in Tampa, Florida, and their reports are meant to help senior U.S. officials and policymakers understand the facts on the battlefield.

Investigators from the congressional task force have met with analysts at both CENTCOM headquarters and, last month, in Washington, half a dozen sources with knowledge of the meetings said.

Spokespersons for the task force declined to comment.

House Intelligence Committee Chairman Devin Nunes previously told The Daily Beast that investigators were unable to obtain certain documents germane to the analysts’ allegations about altered ISIS reports, and that congressional staff had to interview the analysts in the presence of CENTCOM personnel, whom Nunes referred to as “minders.”

“They’re having a tough time talking to us,” Nunes said of the analysts whom congressional staff have interviewed in Tampa.

The Defense Department inspector general is also looking into the ISIS reports. The watchdog’s office has said the investigation, which is expected to be finished soon, “will address whether there was any falsification, distortion, delay, suppression, or improper modification of intelligence information,” as well as “personal accountability for any misconduct or failure to follow established processes.”

At CENTCOM’s intelligence unit, there’s growing anticipation for the results of the Defense Department inspector general’s investigation. Some have said they hope it will hold those they feel are responsible for altering reports, but there’s also concern that the findings will seek to downplay the severity of the problem and won’t lead to any significant changes.

At least one change is in the works. Last week, the Pentagon announced that Maj. Gen. Mark R. Quantock, currently the intelligence director of the U.S.-led military effort in Afghanistan, will take over as the head of intelligence at CENTCOM. Two officials described Quantock as a “straight shooter” who could help relieve tensions at the command headquarters.

Quantock, who is expected to arrive this summer, will replace Maj. Gen. Steven Grove, whom analysts have said is chiefly responsible for altering the ISIS reports. Grove and his civilian deputy, Gregory Ryckman, have also been accused of deleting emails and files from computer systems before the inspector general could examine them, three individuals familiar with the investigation told The Daily Beast.

Investigators from Capitol Hill and the Pentagon’s watchdog have pulled analysts away from work to ask them questions. Their colleagues try to glean insights about the course of the investigation by keeping note of who is being queried and for how long.

And in another sign of rising anxiety, some believe that that military leadership is trying to piece together which analysts have made allegations about Grove, and to whom, whether they be investigators or journalists.