The Air Force investigation, released by the Pentagon, required academy leaders to clarify their policies on appropriate and inappropriate religious expression. But it also credited them with moving to confront these issues.
The investigation also cited a perception of intolerance among some cadets and staff.
"The (Air Force) team found a religious climate that does not involve overt religious discrimination, but a failure to fully accommodate all members' needs and a lack of awareness where the line is drawn between permissible and impermissible expression of beliefs," the report says.
The Air Force team was appointed to investigate the religious climate at the 4,300-student school in Colorado Springs, Colo., after hearing complaints that evangelical Christians wield so much influence at the school that anti-Semitism and other forms of religious harassment have become pervasive.
It assessed Air Force policy on religious respect and tolerance and looked into whether commanders' actions encouraged or discouraged free expression and free exercise of religion.