An Internet user under the name "Blue Cat Polytheistic Religion Founder 07" threatened the tennis player before he arrived to play, prompting organisers to step up security for the Shanghai Masters, which started on Sunday.
"I have not been arrested," said a posting on China's popular baidu.com site, where the original threat also appeared.
"I took the initiative to contact the relevant people to apologise," said the message, which was posted around midday on Tuesday.
The original threat read: "On October 6, I plan to assassinate Federer for the purpose of tennis extermination."
The user also posted a doctored image showing a decapitated Federer on his knees on a tennis court, with an axe-wielding executioner standing next to him.
Shanghai Masters organisers said last week ahead of the competition that they were taking the bizarre threat "seriously" while Federer himself labelled it a "distraction" after arriving in the Chinese commercial hub.
"Obviously maybe it's a little bit of a distraction, there's no doubt about it," Federer said Sunday.
"It was something just very small on a website, nothing clear and concrete, people just debating."
Federer's wife and twin daughters have not travelled to China but he said that decision had nothing to do with the threats.
Federer has been surrounded by a dozen security guards in dark suits who also stayed on the sidelines around the court when he practised on Tuesday. His first match is on Wednesday.
A Shanghai police spokesman on Wednesday declined to comment on the case.
In 1993, former world number one Monica Seles was stabbed by a fan during a match in Hamburg.