Dr Aaron Voon, 41, from Perth, has been charged with possession of child pornography, making child pornography and voyeurism.
Video taken of Voon being confronted by the boy's father and others at the shopping centre, which had a movie theatre, has gone viral on social media.
The incident allegedly took place in Edmonton on May 22.
"These investigations are complex and we have assigned a number of resources to determine if this is in fact an isolated incident," Edmonton Police staff sergeant Stephen Camp, of the Internet Child Exploitation Unit, said in a statement.
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Authorities were called to the West Edmonton Mall just before 4pm when they received a report of an incident at a movie theatre restroom.
Voon was taken into custody and a mobile device was seized at the scene, police said.
Ashley Jackson, who was at the theatre with her son to watch the new Angry Birds movie and saw Voon in the audience, said after the screening she watched the boy's father confront Voon and take the phone off him.
"They were kind of having a little bit of a confrontation and he (the father) kept asking 'Can I just see what's on your phone?'," Jackson told Canada's Global News.
"The father kept putting up his hands and saying, 'No, I need to see what's on your phone - I think I saw you take a video'.
"Then the father of the boy kept saying to his wife 'Well, what's on the phone did you find anything?' and the mother goes 'I'm still looking, I'm still looking' and then after a couple of seconds, you kind of hear her let out this scream and that's when she said that she found the video of her son going to the bathroom ... I won't be able to forget that."
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Edmonton Police detectives want to speak to anyone who may have been within the washroom or the immediate area when the alleged offences took place.
Administrators at Voon's Successful Development and Therapy Centre in Perth reportedly sent an email to clients on behalf of the doctor, WA Today reported.
"A most terrible thing has happened with me in the past week whilst overseas which I will need to manage urgently ... I will have to cease practice immediately indefinitely," Voon wrote.
"For patients and family I am so sorry for leaving you so suddenly. I can honestly state that these issues have been TOTALLY separate from work and I have always provided you and your children with the best possible, safe and appropriate care."
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