Ms Hughes says she was dumbfounded and took the comments as a shot at her son who has autism, and not as a “slut-shaming” slur.
But Senator Thorpe insisted that her comments were not suggestive of Senator Hughes’ son.
“I thoroughly reject any suggestion that I directly or indirectly referenced Senator Hughes’ family,” she said.
“That characterisation of my interjection is completely untrue, and more importantly, harmful to every disabled person.”
Senator Hughes had called the comments in Question Time a disgrace, which came after the Greens senator had interjected an answer about the National Disability Insurance Scheme, and stormed out in protest at Indigenous deaths in custody.
“Have a go at me all you want to, I could not care less,” Ms Hughes told Sky News on Thursday.
“But when someone invokes someone’s child, I think they have crossed a line.”
“Every single person that spoke to me that night in the Senate, every one of my colleagues that heard it took the inference she was referring to my autistic son, that if I had kept my legs shut, I wouldn’t have a child with a disability.”
Senator Lidia Thorpe has taken personal leave from parliament since she made the comments.
Ms Hughes also expressed her disappointment the comments were made a day after a landmark review into the workplace culture of Parliament House was handed down.
“I hope people in this place take stock over the Christmas break,” she said.
“Senator Thorpe needs to think about how she engages with senators.”
It also revealed some of the worst bullying was committed by women against other women.
Liberal Senator Ben Small called out Senator Thorpe’s interjection on the Senate floor, saying the “outrageous” comment ranked at the top of “the scheme of disgusting statements made in this chamber”.
Ms Thorpe initially withdrew the comment, saying: “I just got a view of something over there that disturbed me”.
The senator then returned to apologise to Senator Hughes and unreservedly take back her comments.
The comments also came a day after Liberal Senator David Van was accused of making dog noises towards another female parliamentarian.
Within hours of the release of the Jenkins Review into the sexist culture and harassment in parliament, male members of the government were growling and making dog noises at a female senator in question time.
What is wrong with these people? They just don’t get it. pic.twitter.com/HtmMNT3nV6
Liberal Senator Amanda Stoker said it was important to get the culture right within Parliament House.
“It is important we all lead from the top,” she told Sky News.
“[Senator Hughes] is a tough nut, she will be OK. It is personal and it is not nice. At least Senator Thorpe has apologised.”
Ms Thorpe’s office was contacted for comment.