The body of Adrian Noel Torrens, the alleged killer of 19-year-old Audrey Griffin, was found in his cell at the Metropolitan Remand and Reception Centre in Sydney on Thursday afternoon.
Corrective Services NSW has launched an investigation into the 53-year-old's death.
Torrens was charged on Monday with the murder of Ms Griffin after her body was found partially submerged in Erina Creek on the NSW Central Coast in March.
She went missing after a night out, however police did not initially investigate her death as a potential murder.
Torrens was charged after a four-week investigation into the death of the keen rugby league and water polo player.
It was alleged the pair were not known to each other but were involved in an altercation in the early hours of March 23.
Police later said they were uneasy about attributing Ms Griffin's death to an accident, and fresh information led to murder charges being laid.
A Corrective Services NSW spokeswoman said the death in custody had been reported to the state coroner and would be subject to a public inquest.
"Corrective Services NSW and NSW Police investigate all deaths in custody regardless of the circumstances," she said in a statement.
"Corrective Services NSW extends its deepest sympathies to the family of Audrey Griffin at this distressing time and also sends condolences to any Aboriginal and Torres Strait Islander people affected by Mr Torrens' death."
A spokesman for NSW Corrections Minister Anoulack Chanthivong said thoughts were with those who knew Ms Griffin.
"The minister for corrections acknowledges this very difficult time for the family and loved ones of Audrey Griffin, noting this case will now not be able to be prosecuted through the courts," he said.
Torrens also faced 11 unrelated charges of domestic violence, including using a mobile phone in a harassing or menacing manner and 10 counts of breaching an apprehended violence order.Â
The domestic violence charges were due to return to court in May.
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