Kenjiro Sano, who did not appear at the conference, posted an apology on his website on Tuesday.
While insisting he "never copied or plagiarized" the design, Sano said he "failed to properly handle jobs other than the logo."
That referred to accusations aimed at some of his other designs, including a tote bag found to have used others' images without permission -- a controversy that emerged as Internet users began to dig into Sano's previous work.
Sano said he made the decision to scrap the Tokyo logo in part to "protect his family and staff from criticism and bashings," adding "I have reached my limit where I can no longer endure as a human being."