At 1.30am the next morning she used the toilet and while doing so believed she miscarried the baby.
The woman said she called a hospital worker and asked them to check if it was the foetus.
"She just looked in the toilet, turned around and looked back at me and then quickly flushed the toilet ..."
The woman said she watched what she believed to be her baby get flushed away.
"I said 'Did you just flush my baby down the toilet?'"
The woman said her partner of four years had brought a box to the hospital to put the foetus in.
"We wanted to keep our baby and take it to our marae and bury it, because that's what we do. I wanted to bury it with my nan," she said.
"I feel like something bad is going to happen, like I've broken my cultural protocol. Without having my baby buried. I feel like I've culturally damaged myself," she said.
"Is that what they do when they have miscarriages? Do they just flush whatever comes out down the toilet?"
The woman said she ran back to her room and cried. She or her partner would have been prepared to remove the foetus from the toilet if necessary, she said.
She said she spoke to a senior staff member the next day about what had happened.
"They said they had got an educator up that morning specifically because of what happened to me for them to learn about miscarriages."
The district health board had acknowledged her complaint and told her it was investigating, she said.
The woman's mother was also upset.
"She killed our joy. We wanted to bury the baby with my mother ... so they could be together. That was our only little bit of joy and that's been taken away from us," her mother said.
The Rotorua Daily Post asked the Lakes District Health Board about its policies when women miscarry at the hospital and whether they were given the option to take foetuses home.
It did not answer this, or specific questions about the woman's claims.
Instead assistant communications officer Shan Tapsell said in a written statement: "Lakes DHB received a complaint on Wednesday and an investigation will be carried out as part of our complaints process."