[5] In 1994, the magazine ran what it called an "expose" on what it described as a "history of prejudice" toward minority groups and women by the St. Petersburg Times, a newspaper which the Church of Scientology had some three months earlier accused of "inflammatory" coverage based on "lies and innuendo."

In one case, facts in the magazine's 1995 compilation The Rise of Hatred and Violence, which concerned the church's dispute with Germany, were claimed by Brigitte Schön in the Marburg Journal of Religion to be "grossly distorted.

"[9] Stephen Kent in the Marburg Journal of Religion wrote that the magazine's comparison of the dispute with 1930s Nazism had "general parallels with tactics advocated in the brainwashing manual," Brain-Washing: A Synthesis of the Russian Textbooks on Psychopolitics, published in 1955 by the Church of Scientology.

[10] During Scientology's dispute and litigation against the Cult Awareness Network (CAN), Freedom Magazine was noted for running a sensationalized story headlined "CAN: The serpent of hatred, intolerance, violence, and death.

"[11][12] In their 2006 book Introduction to New and Alternative Religions in America, authors Eugene V. Gallagher and W. Michael Ashcraft cite Freedom Magazine articles about CAN as an example of "the invective emanating from Scientology".