Fan, who took the men's singles title in Paris this year, announced on Friday he was quitting the WTT World Tour, saying he could not "afford" to pay fines under new participation rules.
Fellow Chinese Olympian Chen Meng, the women's singles champion in Tokyo and Paris, also said she would pull out of the circuit.
But in a statement, the WTT said that the rules were "consistent, not new."
"The rules referenced by Fan Zhendong and Chen Meng are not newly introduced," the WTT said in a statement online, adding that they "have been in place since WTT’s inception four years ago".
"We deeply respect the contributions of Fan Zhendong and Chen Meng, two icons who have inspired countless fans and athletes worldwide," it added.
Fan, reacting to the statement, held that he was told the rule would be enforced "from next year".
"When this specifically happened, I’m not sure, but I’m certain that I’ve never been officially informed that I would be fined for withdrawing from competition," Fan said.
"I personally received the official notice last week, that from next year WTT would strictly enforce the newly enacted penalties."
Some Chinese fans reacting to the WTT statement on Weibo compared the tour to an "overlord", with one commenter calling the penalties for withdrawing from competitions "bullying."
According to the WTT, the penalties are in place to "ensure that top-tier players are represented at key WTT events, preserving the integrity of global competition".
Fan did not compete in the recent WTT Finals held in Japan in November, and has not played in WTT competitions since June.
