U.S. military analysts told the nation’s top intelligence official that their reports on ISIS were skewed and manipulated by their bosses, The Daily Beast has learned. The result: an overly optimistic account of the campaign against the terror group.

The complaints, lodged by analysts at U.S. Central Command in 2015, are separate from allegations that analysts made to the Defense Department inspector general, who is now investigating “whether there was any falsification, distortion, delay, suppression, or improper modification of intelligence information” by the senior officials that run CENTCOM’s intelligence group.

This second set of accusations, which have not been previously reported, were made to the Office of the Director of National Intelligence (ODNI). They show that the officials charged with overseeing all U.S. intelligence activities were aware, through their own channels, of potential problems with the integrity of information on ISIS, some of which made its way to President Obama.

The analysts have said that they believe their reports were altered for political reasons, namely to adhere to Obama administration officials’ public statements that the U.S.-led campaign against ISIS is making progress and has put a dent in the group’s financing and operations.

Administration officials have denied that the intelligence reports came under political pressure. But Republican lawmakers and presidential candidates have questioned whether the public is being given an honest account of what effect hundreds of U.S. airstrikes have had on ISIS. The allegations of skewed intelligence have come up in several congressional hearings and figured in an early Republican presidential debate.

The analysts made their claims to the ODNI in response to written surveys that were sent out by its Analytic Integrity and Standards Group last year, as part of a “periodic assessment” to take the pulse of the intelligence community, according to U.S. officials.

Director of National Intelligence James Clapper was asked about the defense inspector general investigation in September during a congressional oversight hearing. At the time, he gave no indication that his own office was aware through its own channels of the analysts’ accusations.

“It is an almost sacred writ… in the intelligence profession never to politicize intelligence. I don’t engage in it. I never have and I don’t condone it when it’s identified,” Clapper told the Senate Armed Services Committee.

But Clapper sought to downplay what he called “media hyperbole” about the substance of the analysts’ complaints. “I think it’s best that we all await the outcome of the DOD I.G. investigation to determine whether and to what extent there was any politicization of intelligence at CENTCOM,” Clapper said.

A spokesperson for the defense inspector general declined to comment for this story.

In the survey from the ODNI, the analysts accused their superiors of editing or rejecting reports that cast doubt on whether the U.S.-led campaign against ISIS was dealing a crippling blow, and they accused senior CENTCOM intelligence officials of attempting to delete emails and other reports that provided evidence of their manipulations, according to a source familiar with the survey who spoke on condition of anonymity.

CENTCOM said no emails were deleted.

“It is important to allow the DoD IG investigation to run its course. However, I can tell you that neither Maj. Gen. Grove nor Mr Ryckman deleted any e-mails associated with the investigation. In fact, as a matter of CENTCOM policy, all senior leader e-mails are kept in storage for record keeping purposes. CENTCOM continues to cooperate fully with the DOD IG investigation,” Air Force Col. Patrick Ryder said in a statement to the Daily Beast.

It’s not clear when the survey responses were reviewed by ODNI officials, but they were included in a report that was finished by December 2015.

The ODNI chose not to investigate the claims of impropriety on its own because the Defense Department’s inspector general had already launched an investigation, sources familiar with the matter told The Daily Beast. That investigation, which hasn’t been completed, began after more than 50 CENTCOM analysts filed complaints with the Pentagon watchdog in July 2015.

U.S. Central Command, based in Tampa, Florida, is responsible for U.S. military operations across the Middle East, from Egypt to Afghanistan. There are more than 1,000 analysts assigned to assessing intelligence and other data on the security situation of the region. They include troops and civilian intelligence analysts who work for the nation’s various intelligence agencies.

The ODNI oversees all intelligence agencies, military and civilian, and is ultimately responsible for ensuring that intelligence reports are free from political influence and bias and that they’re based on sound, verifiable sources of information.

The ODNI standards group was set up by law following the botched intelligence community analysis of Iraq’s weapons of mass destruction program in 2002 (PDF), which suppressed dissenting views that doubted Saddam Hussein had a viable chemical weapons program. That report, which has been effectively disavowed, was seized upon by senior Bush administration officials to make a public case for invading the country.

The standards group “conducts regular periodic assessments of finished analytic products” and reviews them “for timeliness, objectivity and independence from political considerations, and ensures that the products are based upon all sources of available intelligence and employ the standards of proper analytic tradecraft,” Timothy Barrett, a spokesperson for the ODNI, told The Daily Beast in a written statement. “Intelligence analysis from CENTCOM was reviewed by [the group] in 2015 as a part of the periodic assessment, and the information is available to Congress and the [Defense Department inspector general],” Barrett said.

It wasn’t clear whether the congressional committees that oversee intelligence activities had seen the comments from CENTCOM analysts. According to one source familiar with the document, it has been classified at the “secret” level and cannot be widely shared with lawmakers beyond the two intelligence committees.

A task force composed of staff from three House committees—on intelligence, armed services, and appropriations—is investigating the analysts’ allegations and whether they reflect any systemic problems with intelligence analysis.

It remains unclear whether the analysts’ complaints to the ODNI led to any corrective actions or halted what they saw as an inappropriate practice of selectively altering reports. Three sources who are familiar with the defense inspector general’s investigation told The Daily Beast that the watchdog had conducted interviews with analysts at CENTCOM’s headquarters in Tampa, and had reviewed documents allegedly showing that senior officials, including Maj. Gen. Steven Grove, the command’s intelligence director, and his civilian deputy, Gregory Ryckman, had deleted emails and files from computer systems before the inspector general could examine them.

“The cancer was within the senior level of the intelligence command,” one defense official told The Daily Beast. The pushback by the analysts has been described as a “revolt.”

One person who knows the contents of the written complaint they sent to the defense inspector general said it used the word “Stalinist” to describe the tone set by officials overseeing CENTCOM’s analysis.

Two officials at CENTCOM told The Daily Beast they were not aware of the ODNI’s efforts or the survey that analysts had completed. They said the biggest changes to intelligence practices came in the days after analysts filed their complaint with the inspector general. Army Gen. Lloyd Austin, the commander of CENTCOM, urged analysts to speak up if they felt their assessments were being altered.

In the wake of the allegations of politicizing intelligence, some of the people who receive CENTCOM reports told The Daily Beast that they read them more skeptically.

But the reliability of CENTCOM’s analysis has only become more important since the accusations first emerged. In Afghanistan, the Taliban is resurgent and both ISIS and al Qaeda are trying to expand their footprint. In Iraq, U.S. and Iraqi forces pushed ISIS out of Ramadi, raising hopes that the two nations could launch a similar campaign in Iraq’s second-biggest city, Mosul, which serves as ISIS’s Iraqi capital.

In Yemen, ISIS is weaker but al Qaeda is stronger. And in Syria, Russian strikes are helping forces loyal to Syrian President Bashar al-Assad reclaim territory in the city of Aleppo. Should that city fall squarely to the regime, Syria would devolve into a war largely between the regime and ISIS, leaving the Western world with no good outcomes for the fate of that state.

Were that to happen, unvarnished analysis on ISIS and the state of the war would be more important than ever.