Since I am no longer in the Navy and the doctor is not my primary care provider nor physician i contend that he violated my civl rights or at the very least violated HIPPA.
The guidlines for what the doctor is checking for during these physicals is specifically spelled out in the Office of Personnel Management manual (OPM), medical history is not part of the physical.
Guidelines are just guidelines.
If the guidelines call for A, B, and C, and don't specifically prohibit D, I don't imagine that the doctor did anything wrong by addressing D.
With that in mind, read the guidelines again.
It's also possible that, at some point in your employment, you signed something (without understanding it) that authorized the review of your medical history.
It's quite common that people do that, so don't rule out that possibility.