Gatlin who ended this season undefeated and posted season's fastest times in the 100m (9.77) and in the 200m 19.63 seconds was banned for using doping from 2006 until 2010.
"I asked the IAAF to remove me from the list," Harting said.
"I find the nomination great, yet I stand for it alongside a known former doping offender and for that reason I asked to be removed from the list."
Harting says the nomination alongside Gatlin is an insult "not only for me but also for my fans" and says the IAAF should "use honesty in their evaluation" for the award.
"If the IAAF doesn't fully understand the difference, then they should just forget about it," added the 29-year-old, who is currently out injured with a torn knee ligament.
The final event where the athlete of the year will be nominated will take place on November 21 in Monaco.
Men
Nigel Amos (BOT)
Mutaz Essa Barshim (QAT)
Jairus Kipchoge Birech (KEN)
Bogdan Bondarenko (UKR)
Yohann Diniz (FRA)
Justin Gatlin (USA)
Robert Harting (GER)
Dennis Kipruto Kimetto (KEN)
Renaud Lavillenie (FRA)
LaShawn Merritt (USA)
Women
Valerie Adams (NZL)
Genzebe Dibaba (ETH)
Dawn Harper Nelson (USA)
Caterine Ibarguen (COL)
Francena McCorory (USA)
Sandra Perkovic (CRO)
Dafne Schippers (NED)
Kaliese Spencer (JAM)
Barbora Spotakova (CZE)
Anita Wlodarczyk (POL)