The Bay of Plenty Times tried to contact Mr Shipton's lawyer, Bill Nabney, to comment on the allegations yesterday but he did not respond before the paper went to print.
Calls to Detective Inspector Mark Loper, who is now handling a new investigation into Williams' disappearance also went unanswered.
Ms Williams, 26, was last seen at her Munro St home on June 5, 1986.
Her boyfriend, Stephen Prole, who had been with another woman near their home, reported her missing the next day.
Ms Williams had a history of drugs and prostitution and had been in Arohata Prison in Wellington on drug charges.
Ms Bowen claimed Ms Williams had suggested crimes "such as drug dealing were minimised by certain police in Tauranga in return for sexual favours".
Ms Bowen had approached Bruce after an episode of The Investigator about the case. Bruce had handed her affidavit to police and Detective Inspector Loper interviewed Ms Bowen last year.
The Herald reports it is understood she gave further details, including that one of five telephone numbers Ms Williams had put forward for authorisation was checked by Wellington police and found to be a private police number.
Ms Bowen claims Ms Williams said the number was Mr Shipton's.
Mr Shipton was interviewed by police last year as part of an "expanded" inquiry ordered by Police Commissioner Peter Marshall after complaints to the Independent Police Complaints Authority by Ms Williams' family and Bruce.
The other officer Ms Bowen says Ms Williams named was Detective Inspector Phil Seaman. Messrs Seaman and Shipton took over the inquiry into Ms Williams' disappearance. Police initially treated it as a missing-person inquiry, but upgraded it to a murder inquiry in 1994. Mr Seaman concluded Ms Williams had committed suicide. In 2009 he committed suicide after becoming ill.
The police last week announced a $50,000 reward for information in the cold case, citing information new to police that had "taken the investigation in a different direction".
Mr Loper would not confirm to the Herald whether Mr Shipton's role in the case was part of the inquiry. "We have a number of persons of interest," he said. "I will not be drawn into comment about individuals."
The Herald reported that past attempts by prison staff to find Ms Williams' Arohata phone, visitor and bank records were unsuccessful.