Plagiarism from preprint of paper (from the Arxiv)
But while testing plagiarism using free sites we found that results were showing 83% plagiarism from our paper only which is posted on Arxiv. 


Two questions: 


Why did you test your paper for plagiarism in the first place?  I have submitted about 50 papers and have never done this...partly because I never thought of it and partly because I know haven't committed plagiarism because I wrote the papers!  Were you in doubt whether you plagiarized or not?  I don't get it.
If I understood you correctly, you seem concerned that a plagiarism detector found your paper on the Arxiv.  But that's super weird – a paper cannot plagiarize itself, and you are not the first or ten-thousandth person to post their preprint on the Arxiv.  Why would that be a problem?


Based on what you said, it is surprising that you only got 83% plagiarism.  I guess the reason that it's not 100% is that you did make some nontrivial modifications in your paper (and neglected to mention that in your question).  OK, so...I recommend that you post the updated version on the Arxiv.  Then the plagiarism detectors will either figure out what's going on or report that you have plagiarized 100% from a preprint with the same authors and title...a puzzle that even the most harried conference editor should be able to sort out.

Finally, since the question was originally posted on Math Overflow, let me say that in mathematics it would look absurd for a paper to cite its own Arxiv preprint.  If that is actually a halfway standard convention in other fields, I would be very interested to see examples.