The 4.3m estuarine croc was trapped at Cooper Creek, near Thornton Beach in the Daintree National Park, and killed on Friday.
It was taken to a secure Environment Department facility in Cairns for examination, where staff all but confirmed it was the reptile responsible for taking Ms Waldron on Sunday night.
"At this stage police believe the remains are those of a woman who was reported missing on May 29," police said.
"Police will be preparing a report for the coroner."
It was the second croc to be caught in the area after authorities set three traps as they continued to search for any trace of New Zealand-born Ms Waldron, a longtime NSW resident.
The 46-year-old was dragged under the surface during a late-night beach adventure with friend Leeann Mitchell, who had tried desperately to save her.
Ms Waldron's father Pat and sister Anna-Lee Annett flew to Cairns from New Zealand this week to be closer to where she spent her final days.
They made an emotional visit to Thornton Beach to say goodbye after expressing gratitude for the massive search effort.
"We need to be here and cry on the beach," said Mr Waldron, who did not want the crocodile harmed.
He said his daughter would often do "crazy things" and would have known about the risks.
The fatal attack has prompted the state government to allocate an extra $5.8 million over three years for comprehensive population surveys and crocodile management.
Environment Minister Dr Steven Miles admitted the government did not know with scientific certainty whether croc numbers were rising or falling in some parts of the state.
