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Just a wild guess here, was this government agency the NSA?  You should file a Freedom of Information Act / Privacy Act (FOIA/PA) request.  I forget which one it is but it looks like there is an online form at each of those links and the postal mailing addresses are the same.  

Satirically, the street name of the NSA FOIA/PA office is Savage Road.  A befitting name for how the intelligence community mistreats their applicants during the pre-employment polygraph interrogations.

It will take several months but you will get a thick file on everything the NSA has on you.  The pertinent information in the FOIA/PA documents that you receive back, including the polygraph report, will be mostly redacted. However, it will help you discern exactly what absurd reason the NSA had for rejecting you.  

If you had your security clearance denied, then the NSA is required to tell you exactly why and you can appeal.  If you were just found unsuitable, then you have to figure out the reasons yourself based on your recollection of the events during your polygraph and psychological processing and the information you obtain from the FOIA/PA office.