The complaint was filed by The Traveller Equality and Justice Project (TEJP) at the Centre for Criminal Justice and Human Rights at UCC.
TEJP lodged the complaint with the council's ethics registrar as Cork City marks Traveller Pride Week.
Specific details of the complaint have not been revealed by either TEJP or the council.
Independent Cllr O'Flynn, of the city's North East ward, said he is aware of the complaint, which he called "another effort to silence any critics" of the Traveller community.
"This movement, and those like them, have one thing on their mind - to silence their critics and anybody who has an opinion which differs from theirs," O'Flynn said. "Whenever I have spoken on the Spring Lane (halting site) issue, I’ve only listed facts. This complaint won’t stop me from doing my job - and that is to represent everybody, including those who live on this halting site."
Cllr O'Flynn said that he has received abusive phone calls and letters, and even a death threat issued over the phone.
"They told me they were digging a hole for me," he said of the threat. "I reported it to gardaí. I’m not losing any sleep over it."
Cllr O'Flynn drew criticism after accusing Traveller advocacy groups of ignoring issues at the Spring Lane halting site, including illegal dumping.
Residents of the site have accused O'Flynn of spreading "deliberate, hurtful, false information" and using "almost every imaginable anti-Traveller stereotype" to "turn the people of Cork against" them.
