Independent senator Nick Xenophon last week said correspondence from former members had implicated the church in a range of crimes, including forced imprisonment, coerced abortions, intimidation and blackmail.
Eight letters from former members of the church were tabled in Parliament, including one from Paul David Schofield, who said his toddler daughter Lauren fell down some stairs to her death after being allowed to wander around one of the church's Sydney buildings.
"My wife and I were actively discouraged from seeking compensation from the church," he wrote.
"I was also encouraged by church executives to request no coronial enquiry into her death, something I stupidly agreed with at that time."
But the church today said the allegations were false.
"Based on detailed evidence, deputy state coroner Jacqueline Milledge ruled that Lauren's death was an accident and that an inquest was unnecessary," the church's spokeswoman, Virginia Stewart, said in a statement.
Ms Stewart also rejected suggestions Lauren was allowed to wander around the stairs while under the church's care.
"Two witness statements attest that Lauren was in the care of her father, Paul Schofield, and three teenagers at the time of the accident," she said.
"She was not wandering the stairs by herself but rather walked to the top of the stairs while she and a group of small children were being moved from one room to another, under close supervision.
"Both witness statements clearly attest that Paul Schofield was a matter of a few metres from his daughter when she fell down a flight of stairs."
Ms Stewart also rejected claims church executives pressured Mr Schofield not to request a coronial inquiry.
"Based on detailed evidence, deputy state coroner Jacqueline Milledge ruled an inquest into Lauren's death was unnecessary.
"Senator Xenophon has exploited this personal tragedy and made some shocking and untrue allegations to impugn the reputation of the Church of Scientology."