The German, who also holds the world and European titles, is among 10 male athletes nominated for the award along with American Gatlin, who set a world's best time of 9.77 seconds in the 100 metres this year.
However, Harting does not want to be associated with the sprinter, who served a four-year ban for doping offences between 2006 and 2010.
"I ask the IAAF to remove me from the list," Harting said.
"I find the nomination great. Yet I stand for nomination with a former doping offender, and that is the reason for my waiver."
Voting for the award is open to athletes, officials, member federations and media until October 16.
The winner will be announced by the IAAF's ruling council on November 21 in Monaco.