In Weaver's book, What Am I Supposed to Eat? it suggests pregnant women consume folate to reduce the risk of "neural tube defects, spina bifida, deformed limbs and mongolism".
IHC, an organisation that advocates for children with intellectual disabilities, was "thrilled" Weaver had pulled the book from shelves.
Director of advocacy, Trish Grant, said the connection made between Down syndrome and folate had an "extraordinary lack of basic science".
"Down syndrome has nothing to do with folate.
"I think the comments are not only inaccurate but also distressing. They have potential to cause a lot of unnecessary harm," Grant said.
She said the gaffe was the kind of misinformation that added to poor attitudes around Down syndrome.
Weaver is expected to publicly apologise for the mistake, and has said anyone who bought a copy of the book can return it for a refund.