The review found 90 percent of the 195 U.S. dioceses were carrying out all of the new plan, which was adopted by U.S. Catholic bishops at their 2002 meeting in Dallas as a response to hundreds of allegations of sex abuse by priests.
The policy bars priests who have molested children from active ministry, such as performing Mass or teaching in parochial schools. It also puts safeguards in place to prevent molestation, such as conducting background checks on all diocesan priests and lay workers and training them to identify abuse.
Among the 20 dioceses found to not be in full compliance are the archdioceses of New York; Anchorage, Alaska; and Omaha, Neb. Four dioceses were not audited.
The church commissioned the report from the Gavin Group of Boston. Kathleen McChesney, a former top FBI agent and head of the bishops' Office of Child and Youth Protection, oversaw the investigation.
Some victim advocates said bishops had too much control over how the audit was conducted.
"Essentially, bishops have defined the rules of the game, decided who plays, paid the umpires, and are now declaring themselves the winners," Barbara Blaine, president of Survivors Network of Those Abused by Priests, said in a statement posted Monday on the group's Web site.
"In most audits, investigators can compel access to objective data -- bank statements, legal documents and the like. In this case, the interviewers had to rely largely on subjective material that was given voluntarily, and given by essentially the same men who have, for decades, fought to keep the crimes of clergy concealed," Blaine said.
Steve Krueger, executive director of Voice of the Faithful, an organization formed in response to the sexual abuse scandal, said that the audit provided a "foundation to build upon." However, he added, "The audits only provide a narrow test of the issues that need to be addressed in protecting children, providing justice for survivors and restoring trust in the Church."
According to the report, auditors did not view personnel files that would verify whether bishops were complying with the policy's ban on transferring offenders from one diocese to another.
However, William Gavin, president of the Gavin Group, insisted the audits were comprehensive and accurate. Investigators did not view personnel records due to "sensitivity to laws and privacy violations that may occur." Otherwise, he told the Associated Press, "We had free rein."
The auditors -- mostly former FBI agents or investigators -- visited dioceses from June to October in small teams, interviewing bishops, diocesan personnel, victims, abusive priests, prosecutors and lay people.
The review was meant to help enforce the Church's reforms and will be conducted annually.
Under church law, there is no mechanism to sanction those who don't comply with the new policy because each diocese is autonomous and bishops answer to the Vatican, not each other.
Gavin said most of the instances of non-compliance resulted from confusion over how to abide by the new rules.
"For the most part, it was not a refusal to adhere to the policies it was a lack of understanding of how to do so," Gavin told the AP.
The auditors also concluded the bishops needed to improve their outreach to victims of priest sex abuse, which is required under the policy.
"We have a long way to go in that area," McChesney told the AP.
A second study the bishops commissioned is scheduled to be released Feb. 27and attempts to tally every church abuse case in the country since 1950.