"Pregnant prisoners are not compelled to share a cell if they don't wish to,"he said.
"They are always allocated a built bed. However decisions about their accommodation arrangements do take into account their individual wishes,and their best interests.
"The general manager personally reviews the accommodation arrangements of pregnant prisoners at least weekly."
Mr Clarke said QCS had taken to doubling-up prisoners as a means of managing overcrowding.
"In many cases,this means one of the prisoners must sleep on a mattress on the floor with her head close to an exposed toilet,"he said.
"This practice substantially impacts on a prisoner's privacy and dignity.
"Prisoners who are doubled-up experience less favourable living conditions than those in single cells.
"I am of the view that the extent of overcrowding at BWCC means female prisoners in south-east Queensland are being treated less favourably than male prisoners.
"I consider this is improper discrimination against female prisoners in Queensland."
Mr Clarke said there has also been a"significant increase"in the incidents of assault,self-harm and attempted suicide at BWCC.
Mr Byrne said the Ombudsman's report did not reveal anything that was not already known and he was confident about the level of safety and security at prisons.
Announcing a $1 million reintegration package for female prisoners,Mr Byrne said the Palaszczuk government would focus on diversionary programs in its attempts to manage overcrowding,rather than expanding existing prisons or building new facilities.
"If the decision was made tomorrow to build more facilities in Queensland,there wouldn't be a cell opened for three years,"he said.
"That's a fact,no matter if you think we're going to build our way out of this current circumstance.
"...There are no short-term fixes for building new prisons.
"What we are endeavouring to do is make sure the people who deserve to be behind bars are behind bars and we're endeavouring to make sure that people who can be diverted from becoming institutionalised in mainstream prisons are diverted."
Shadow attorney-general Ian Walker said it was a damning report that needed to be addressed and Mr Byrne's response was too dismissive.
"We in the LNP don't expect prisoners to be housed in the Taj Mahal,but we do expect that they will be in proper and decent conditions because if they're not,it leads to considerable discipline measures in our jails,"he said.
"If our prisoners are not housed in proper,decent conditions,then it puts our hard-working prison officers at risk because of the unrest that leads to in the prison system."
Mr Walker said prison overcrowding was a safety issue,rather than concerns about the comfort of prisoners.