The 28-year-old, whose real name is Tyler Blevins, is one of the most popular video game personalities in the world and boasted more than 14 million subscribers on the Amazon-owned platform.
He cut ties earlier this month to sign an exclusivity deal with Mixer, a rival website run by Microsoft, and since then his old channel has been used by Twitch to advertise other streamers in his place.
In a video posted on Twitter, the multimillionaire said he was now trying to get his abandoned profile taken down following concerns that his younger fans could have been among those exposed to adult content, which Twitch has acknowledged "grossly violates our terms of service".
Ninja - who has earned millions of dollars by playing Fortnite - added he had "let slide" some of the changes made to his old channel, including his verification badge being removed, but said a line had been crossed.
He said: "I've been streaming for eight years to build my brand and build my channel, 14.5 million followers, and they were still using my channel to promote other streamers. Now there was a porn account that was number one being recommended on my channel and I have no say in any of this stuff.
"We're trying to get the channel taken down, or at least not promote other streamers and other channels on my brand and my profile. If anyone saw that, for anyone's kids who saw that, I just wanted to apologise - I'm sorry."
Twitch chief executive Emmett Shear has apologised to Ninja over the "lewd content" that appeared on his channel, which he said there were "no excuses" for and that it "should not have happened".
He said the account in question had been suspended.
Ninja has since thanked Twitch for restoring his channel "back to how an offline page should look", but Mr Shear has indicated that visitors to the profile will soon continue to be given recommendations for other channels.
In a statement posted on Twitter, he said: "Our community comes to Twitch looking for live content. To help ensure they find great, live channels we've been experimenting with showing recommended content across Twitch, including on streamer's pages that are offline. This helps all streamers as it creates new community connections."
Ninja, who also has more than 22 million subscribers on YouTube, amassed more than one million followers on Mixer within a week of joining the platform, which is a much smaller service than Twitch.
According to TechCrunch, it accounts for just 3% of the time spent by people watching video game streams online, compared to 72% for Twitch.
Despite the number of hours Ninja has spent honing his Fortnite skills in front of a live audience, he failed to qualify for the recent Fortnite World Cup.
Among the finalists was a 15-year-old boy from Essex, Jaden Ashman, who won a $2.25m (£1.8m) prize with his teammate after the pair finished second.