"While I'm sorry to be leaving, the pre-existing commercial framework makes it difficult for me to apply my talents and fully leverage the assets of the IAAF in the way I would like," said Gers.
"Given my stance, I have resigned so the IAAF can pursue a different commercial strategy for the sport."
The IAAF said Gers would continue in his role for the next three months after which a new CEO would be recruited.
The news is another blow to IAAF President Sebastian Coe in what has been a difficult period for the Briton and his organisation.
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Coe was criticised this week by a British parliamentary report for providing "misleading" answers to questions in a 2015 hearing about what he knew about doping in Russian athletics before he took office.
Coe, who was elected IAAF chief in 2015, had previously denied misleading the committee.
"I would like to thank Olivier for the work he has done particularly around putting a strong team in place at the IAAF, developing a strategic plan and securing broadcast and digital rights to expand audiences for Athletics globally," Coe said.
"Coming off the best world championships we have ever had, having established a set of reforms that solidly underpins the governance of the sport and having established a solid foundation for growth, we will move forward with the innovation that will bring in new fans and new partners."
Despite the success of last year's world championships in London, Coe has a challenging task to restore the reputation of his sport given the fallout from the findings of the 2016 McLaren report into widespread doping by Russia athletes.
The Russian athletics federation remains suspended by the IAAF.
Losing a CEO tasked with broadening the global commercial appeal of athletics will be seen as another setback, particularly in an era without the attraction of Jamaican sprinting great Usain Bolt who retired last August.
(Reporting by Shrivathsa Sridhar in Bengaluru and Christian Radnedge in London, editing by Ed Osmond)
