An extensive search of the surrounding drains by a specialist police team resulted in other parts of the skeleton being found.
Detective Inspector Bruce Scott said last night that forensic examination resulted in the positive identification of Ms Chen's body.
No arrest had been made and the investigation was ongoing.
Mr Scott said the discovery of Ms Chen's body was a significant breakthrough in the investigation.
"The area that Cissy's body has been found in was well-known to both Cissy and her partner. They lived nearby and used to walk regularly around the neighbourhood," he said.
"We're now working through the information gathered from last week's scene examination, and an area canvas of residents in the neighbourhood is also underway.
"Anyone who lived in the Totaravale Reserve area in November 2012 who has since moved is asked to get in touch with us."
Mr Scott said police had spoken with Ms Chen's family and whilst they were understandably upset, they were pleased that her body has now been found.
A blessing of the site where the remains were found will be performed by a local Kaumatua tomorrow morning.
Last year Mr Scott told the Herald that police believed Ms Chen was killed at or near her property. Despite an extensive search, which included parks, waterways and building sites, no trace of Ms Chen was found.
"That led us to believe that she hadn't been out walking. Nobody had seen her. It was a night that lots of people were out and about, but no one saw her that night."
She was last seen leaving the accountancy firm where she worked on November 5, 2012. She drove to her home in Torbay on Auckland's North Shore, went inside and wasn't seen again.
Her partner, Yun Liu, known as Jack, reported her missing at 9.30 that night, saying she had left the house to go walking at 5.30pm and had not returned.
He usually walked with her, but told police he had injured his leg so had stayed home.
