Washington (CNN) -- A long-awaited report on alleged misconduct within the Federal Air Marshal Service concludes that while supervisors do not engage in "widespread" discrimination and retaliation against rank-and-file air marshals, the agency is far from trouble-free.
The report, from Department of Homeland Security's Office of the Inspector General and obtained by CNN, paints an unflattering picture of the agency, saying air marshals share the widespread "perception" that they are being mistreated, and adding that investigators "heard too many negative and conflicting accounts" of misconduct to dismiss them.
"Federal air marshals repeatedly portrayed their supervisors as vindictive, aggressive, and guilty of favoritism," the report says.
A "substantial percentage" of air marshals surveyed believe they are victims of discrimination or unfavorable treatment. And many fear retaliation if they report violations of laws or regulations, the report says. "There is a great deal of tension, mistrust and dislike."
At the same time, the report says, rank-and-file air marshals share in the blame. Air marshals with grievances sometimes take their bosses' actions out of context, fail to disclose the whole story, and misinterpret management decisions as harassment, the report says.
Importantly, the report says, the divisiveness and tension on the ground "do not appear to have compromised" the agency's mission" in the sky.
The 21-month investigation was triggered by a January 2010 CNN report about air marshals based at the Orlando, Florida, field office.
An air marshal there alleged that supervisors created a "Jeopardy"-style game board and labeled it with terms such as "pickle smokers," "our gang" and "creatures," which, he said, alluded to gay men, African-Americans and lesbians. The names ridiculed air marshals who had fallen out of favor, and targeted them for retaliation, he said.
But the Office of the Inspector General says it "found no evidence" that the board resulted in unfair treatment of air marshals.
The report says the game board was created by three people -- a supervisor, an air marshal and a civilian training officer. The air marshal said the "Jeopardy" board was used to make fun of the training staff, not others. And he provided "relatively innocuous explanations" for the terms used on the boards, the Office of the Inspector General said.
But a training staff member, who was not involved in the board's creation, gave a different explanation. He said the training staff "used the game board to make fun of federal air marshals they disliked, including African-Americans, gays and lesbians, and others who had filed complaints against the office," the report says.
All three people responsible for creating the board have left the agency, it says.
Though the game-board disclosure triggered the inspector general's investigation, the scope of the investigation expanded as air marshals stepped forward with other allegations about their bosses. More than 300 people were interviewed, and investigators visited Air Marshal Service offices in Orlando and Tampa in Florida; Charlotte, North Carolina; Cincinnati; Minneapolis; and Dallas.
The degree of animosity varied at different field offices, according to the report, which called the animosity at Orlando "unsettling."
"We conducted numerous interviews at offsite locations because interviewees did not want to be seen talking to us," the report says.
It says the inspector general's office received numerous individual allegations of misconduct, but did not investigate them, leaving open the true extent of the mismanagement.
"Determining whether one employee retaliated or discriminated against another is a complex matter" that would require a court to determine, the report says.
A Federal Air Marshal Service spokeswoman contacted by CNN late Thursday reiterated that the report found no evidence of widespread discrimination or retaliation. Employees' perceptions of discrimination stem from poor communication with the work force, she said.
"While the (agency) faces organizational challenges, the (inspector general's office) notes that these challenges do not interfere with the mission of the agency," Kimberley Thompson wrote in an e-mail statement. "Through working groups, listening sessions, and advisory councils, (Federal Air Marshal Service) leadership has demonstrated its commitment to improving communications within the workforce."
She added the Transportation Security Administration "took a proactive approach to the issues raised and has developed and implemented solutions ahead of the conclusion of the investigation."
But Tom Devine of the Government Accountability Project, a nonprofit whistle-blower organization, called the report "a significant vindication for air marshal whistle-blowers."
"It confirms a perceived pattern of retaliation against air marshals who challenged security breaches by Federal Air Marshal Service management," he said.
The inspector general's report puts a spotlight on common complaints that many air marshals have against their supervisors, and vice versa. Many air marshals "harbor strong feelings" that former U.S. Secret Service employees, who flooded the top ranks of the agency following the September 11th terrorist attacks, created their own "elite culture" within the agency that was not held accountable. Conversely, supervisors "did not hide their view" that the government, in its haste to create the agency, hired unqualified people, the report says.
The government investigators said they identified factors that contributed to the allegations of a hostile work environment. There was limited transparency to management decisions, it said, and there is limited interaction between managers on the ground and the officers, whose job requires extensive travel.
The report said the TSA and the Federal Air Marshal Service are committed to addressing the factors that led to the investigation and the problems that air marshals say still exist.
The inspector general recommended the TSA "create and implement an action plan" to address workplace issues. "The plan should include training for supervisors on communication and conflict management that is tailored to the unique Federal Air Marshal Service mission," the report stated.