Q - May an employer copy documents presented for I-9 purposes?
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A - The law does not require nor prohibit the copying of documents presented for I-9 purposes.  As the INS Handbook for Employers states on page 15:
The law does not require you [an employer] to photocopy documents.  However, if you wish to make photocopies, you should do so for all employees, and you should retain the photocopy with the I-9 [there is a different rule for employees of the Federal government concerning where such photocopies should be retained].  Photocopies must not be used for any other purpose.
Note:  if an employer chooses to photocopy documents presented, it is important that s/he photocopy the documents of all new hires, not just those s/he may think are aliens.  To do otherwise, may subject an employer to a charge of unfair immigration related employment practices.