What can be done about being disqualified from MEPS based on paperwork alone?

I don't know if it's different with the Navy, but with the Army there can absolutely be different fitness for duty standards for initial enlistment/appointment (Chapter 2 of AR 40-501) versus retention (that would be Chapter 3). In other words, if you're already in the military, a condition/surgical history/etc. might not get you kicked out but could be the kind of thing that prevents you from joining. Since this is switching to a new branch of the military, my guess is they're using the accession and not the retention standards, so it sounds like that's the weird limbo you're in right now. I would definitely want more information from the recruiter...is it merely the fact that you had a surgery that made MEPS DQ you, or is it presumed (or actual) limitations or after-effects following the surgery?

Good luck!

http://www.usphs.gov

Call [login to see] and chat with the USPHS recruiters about PA, as well as Jr and Sr COSTEP, their analogue to ROTC, it may be allowed for grad level, as ROTC is, I'd read. Next, I'd very definitely purely as a suggestion, maybe also submit the whole thing to your Congress offices, House and Senate, all three, they'll want Privacy Act (PA) forms, it's the law, they can't help you without them. USPHS has sites about a cooperative program with the other svcs, esp for those who want psych related, I'm not saying you want psych PA, it:s merely an FYI...that being said, how far are you into the 2 yrs of PA, also, what's your GPA, and ypwhat are your actual grades, if you can say, knowing that could help myself and others suggest stuff...did you start rotations yet at all? Do you want PhD level at all? Research interests? Is the PA a masters level program? Most are, I'd just wondered...also, if so, what specific clinical areas did you want? OR at all? How much actual OR time have you had thus far, and what class.type of procedures? I was doctoral level allied health, we shut my license sevl yrs ago, due to total perm disability, I just had interest in career/educ topics...look up also the PhD programs at USUHS, not USPHS, the svc, I'm speaking now of the school, the PhDs in infectious disease, neuroscience, and molec cell bio can be attended on civilian tracks, though one can also try for active duty attendance, they also have an online certificate program, it's really jammed with applicants, for preventive med, only for active duty Guard, and Reserve however, I did check about those PhD programs, they do have civilian tracks, and, what was your assocs and/or Bach in, also, what grades and/or GPA as well, no rush, I'd be eager to hear more, the whole disqual thing, I'd seek to appeal it through your Congress offs, as I'd said, just a suggestion, out understand...as you explain the problem, it is unusual, certainly...I'd also be curious about more on the foot surgery you'd mentioned, there's a limit to what I could suggest, of course, however, the circumstances, as you relate them did interest me, certainly if I can suggest anything else, I'll certainly try, you might also ask yur own Reserve chain for any possible help getting further clinical eval and/or endorsement, it'd help to know of you've asked anyone in your unit, thus far, at all...explain as much more as you can, I'll try to reflect on the whole thing further, OK?

The apparent “double standard” for fitness is actually normal for the military. There are many folks who are amputees due to war time injuries who are still in the military. But no service would ever accept a new recruit with an amputation.

The waiver is your only hope. Or wait a bit and reapply later.