Senior intelligence officials at the U.S. military’s Central Command demanded significant alterations to analysts’ reports that questioned whether airstrikes against the so-called Islamic State widely known as ISIS were damaging the group’s finances and its ability to launch attacks. But reports that showed the group being weakened by the U.S.-led air campaign received comparatively little scrutiny, The Daily Beast has learned.

Senior CENTCOM intelligence officials who reviewed the critical reports sent them back to the analysts and ordered them to write new versions that included more footnotes and details to support their assessments, according to two officials familiar with a complaint levied by more than 50 analysts about intelligence manipulation by CENTCOM higher-ups.

In some cases, analysts were also urged to state that killing particular ISIS leaders and key officials would diminish the group and lead to its collapse. Many analysts, however, didn’t believe that simply taking out top ISIS leaders would have an enduring effect on overall operations.

“There was the reality on the ground but it was not as rosy as [the leadership] wanted it to be,” a defense official familiar with the complaint told The Daily Beast. “The challenge was assessing whether the glass was half empty, not half full.”

Some analysts have also complained that they felt “bullied” into reaching conclusions favored by their bosses, two separate sources familiar with analysts’ complaints said. The written and verbal pressure created a climate at CENTCOM in which analysts felt they had to self-censor some of their reports.

Some of the analysts have also accused their bosses of changing the reports in order to appeal to what they perceived as the Obama administration’s official line that the anti-ISIS campaign was making progress and would eventually end with the group’s destruction.

Lawmakers and even presidential candidates seized on the allegations of politicizing intelligence as the White House tried to distance itself from the very strategy it has been pursuing.

Army General Lloyd Austin came under withering bipartisan criticism on Wednesday when he testified before the Senate Armed Services Committee that after spending at least $43 million over a 10-month period, the U.S. had trained only nine fighters to confront ISIS in Syria.

Senators were dumbfounded that the nearly year-long effort had produced such paltry results, calling it “a joke” and “an abject failure.”

Senator John McCain, the committee chairman, called Austin’s testimony “grossly distorted” and said the general was attempting to convince senators that the military was making more progress against ISIS than he believes it is.

Asked whether he had ever ordered changes to intelligence reports, Austin replied, “Absolutely not.”

The Obama administration is now considering modifying the Syrian train-and-equip program, while the White House attempts to portray the president as having always been skeptical of it.

Meanwhile, Pentagon investigators are examining the back-and-forth between the intelligence bosses at CENTCOM and the analysts, which created a paper trail. Favorable reports had fewer comments written on them, and requests that were more critical showed heavy questioning, the two officials said.

The altering of intelligence led to reports that overstated the damage that U.S. strikes had on specific ISIS targets. For instance, strikes on oil refineries and equipment were said to have done more damage to the group’s financing of operations through illicit oil sales than the analysts believed. Also, strikes on military equipment were said to have set back the group’s ability to wage combat operations, when the analysts believed that wasn’t always the case.

The altered reports made ISIS seem financially weakened and less capable of launching attacks, the analysts allege.

The CENTCOM supervisors “did not like the reports on the impact [of the airstrikes] because they didn’t believe it,” one military adviser familiar with CENTCOM operations told The Daily Beast.

The Defense Department inspector general has been conducting interviews at CENTCOM headquarters in Tampa, Florida, in order to determine who in the command’s intelligence directorate may have distorted or manipulated the intelligence reports, some of which eventually made their way into materials briefed to President Obama. Investigators have pulled CENTCOM personnel one by one into private interviews to get to the bottom of the allegations and determine who was ultimately responsible for changing intelligence reports, according to individuals with knowledge of the investigation.

The inspector general has confirmed that the investigation is focused on the CENTCOM intelligence directorate, or J2. Multiple sources told The Daily Beast that the head of intelligence, Army Major General Steven Grove, is named in the complaint, as are several other senior officials at CENTCOM. The tone of the complaint is said to be harsh and highly critical of senior officials’ leadership and actions.

The U.S.-led coalition to fight ISIS has conducted 6,863 strikes in the year-long campaign in Iraq and Syria, according to Pentagon statistics.

No evidence has emerged that military commanders at CENTCOM who make decisions about airstrikes read the reports and then changed the number of strikes as a result. However, the generally optimistic reports may have stalled debate about whether the strategy needed to be re-examined or changed.

Defenders of CENTCOM noted that however optimistic the reports were, they are just one of many factors commanders would have considered when assessing a strategy. A CENTCOM spokesman said that while he couldn’t discuss ongoing investigations, there’s a robust system of assessing information, and it doesn’t rely solely on one assessment.

“The intelligence community routinely provides a wide range of subjective assessments related to the current security environment,” said Air Force Colonel Patrick Ryder, a CENTCOM spokesman. “Senior civilian and military leadership consider these assessments during planning and decision-making, along with information gained from various other sources, to include the insights provided by commanders on the ground and other key advisers, intelligence collection assets, and previous experience.”

The Pentagon investigation has led some CENTCOM analysts to fret that launching their complaint will end up tainting the credibility of their reports for years to come, the very thing they were trying to avoid by calling out their bosses.

Still others worry that the inquiry, which could take a year, will not aggressively seek to hold accountable those who changed the reports.

Several sources told The Daily Beast that Austin has warned his subordinates not to retaliate against anyone who spoke out, helping mollify a tense environment at CENTCOM.

The alleged cooking of the intel books on ISIS became a point of discussion in the second televised Republican presidential debate last week.

Former Arkansas governor Mike Huckabee pointed to the CENTCOM analysts’ complaint during a discussion of national security strategy. “If you don’t have good intelligence that is reliable and honest, you won’t have good intelligence and you cannot make good decisions,” he said.