If they told you to reapply in a year or two, then it is not a permanent disqualification.  I personally would apply at other departments and explain the failed polygraph to the new department, then take a new polygraph with the new department you are applying for.  "Most" agencies allow this and don't discriminate against you for the failed exam with another department.  If you ask before applying, I'm sure they will guide you through their process.  Good Luck

I am sorry for misunderstanding your post.  I was talking about a different department such as FBI to ATF, DIS, or other agencies, not the same agency.  Just a side note, did the agency you applied for offer you a retest?  Most federal agencies will retest if requested.

I took the polygraph in 2012 for CBP and after six hours was told I failed, a retest was denied.  I believe the the examiner stated I tried to tamper with the results which is not true.  I have replied multiple times but have never made it through the assessment phase once the results of the test were brought up.  What makes it worse is that this will show up in Background check for other agencies and unless you can supply evidence of mismanagement they may still use the failed results as a reason to disqualify you.   

I'm still trying.  Somewhere some common sense will come up.