Politicians on all sides have condemned the comments as ill-informed.
And Australians with autism are calling for better understanding and support for children in mainstream schools.
Pauline Hanson's comments on children with autism have riled politicians from across the political spectrum.
And for Labor MP Emma Husar, whose 10-year-old son has autism, it was personal.
She had this message for autistic children across Australia.
"And even on the days that are hard, when you're frustrated and your disability makes you angry, you are still better than she is on her best day."
Greens MP Adam Bandt has called Senator Hanson's comments "hateful, outrageous and disgraceful."
"Having children in schools who have special needs, it isn't just important that those children are able to attend those schools. It's good for the other kids in the classroom, who learn that, if we are in a civilised society, where there is difference, we should accept and celebrate that difference, because that is what makes us a decent society."
They were responding to these comments a day earlier from the One Nation leader.
"Whether they have a disability or whether they are autistic, that is taking up the teacher's time. Consider the impact that is having on other children in that classroom."
Autism Awareness Australia chief executive Nicole Rogerson says the suggestion children with autism should be separated from their classmates is ill-informed.
She says research suggests the opposite approach.
"The best place for children with special needs is in their community, in their local school, and we need to support them accordingly."
Senator Hanson is not backing down, though.
"Look at the problem that we have. There are different grades of autism."
She has refused to apologise to people with autism who found her comments hurtful.
That includes people like Ben Carbonaro, who went to a mainstream school and on to further education, graduating with a degree in journalism.
"(I'm) upset and frustrated, because, those of us on the autism spectrum, all we want is inclusion and acceptance within the wider society."
Amy Smith, studying for a bachelor's degree in disability and inclusive education, says she does not believe she could be in that position if she had been separated from classmates.
"The ability to mix with non-autistic children from as young an age as possible can actually help them to apply a lot of what they learn in the therapist's office ... On top of that, there is also a benefit to many children who are not necessarily living with disabilities. They learn to work with people in the future. Life outside the school, especially if you live in one of the major cities, is incredibly diverse."
She says she wants to see better awareness and acceptance of people across the autism spectrum.
"We are different. We're not defective, though."
