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Now, two months on, the number of such alerts has decreased to just a couple a week, but the web safety group Netsafe says such material is still available on almost 50 websites worldwide.
And, as a Wellington man discovered, the manifesto and references to it can turn up in the most unexpected places.
The man, whom RNZ has chosen not to name, was watching an American welder on YouTube demonstrating various repair techniques, when he went off topic.
"There was a video entitled 'They banned this book so I'm going to read it to you', so I clicked on the link and he started talking about something ... it looked pretty darn boring and went for over two hours so I clicked off and went somewhere else."
A few days later the Wellingtonian returned to the welding website, which had a new video titled 'They're deleting my channel'.
When he clicked on it the man discovered the American welder talking about the Christchurch gunman and it soon became obvious the "banned book" he'd earlier referred to was the shooter's manifesto.
"And I thought that wasn't particularly good. He made some derogatory comments about Muslims.
"He was basically just being some sort of right-wing weirdo so at that stage I passed on information about that video and the previous one, now that I'd worked out what it was, to Internal Affairs."
The man said he received a message from Internal Affairs saying they had taken down both videos, but he was alarmed last week to discover other Youtube users have made mirrored versions and the material was still available.
Netsafe's Martin Cocker said it was pretty unusual to find something illegal or offensive when browsing a regular site on the internet, but people were becoming more adept at finding ways around online censors.
"It's becoming increasingly common for people to splice into videos something that's offensive or harmful - it shouldn't be there.
"If you put the video up in and of itself it gets detected and found really quickly, but if you hide it in the midst of something else it's more likely to survive for longer on platforms like YouTube."
You can't completely delete something from the internet
The Department of Internal Affairs' director of regulatory systems, Jolene Armadoros, said removing material like that relating to the Christchurch attacks was a bit like a game of whack-a-mole.
"We found that people would upload different versions of the video, making it harder to auto-detect ... and in the case of someone reading the document verbally, versus posting it, [that] makes it harder again to go and find.
"The reality is you can't [totally] delete something from the internet."
Ms Armadoros said there were two things anyone stumbling across material relating to the Christchurch terror attacks online could do, including reporting it to the platform they found it on.
"In most cases this kind of content actually breaches the terms and conditions of those platforms, even sometimes where it doesn't breach law; so it's really important to have that reported.
"If they're not satisfied with the response, or if they're not sure whether it's something that's not allowed to be shared, getting in touch with us is really useful because we can follow that up on their behalf."
Ms Armadoros said the best advice she can give internet users is 'think before you share'.