This week, Prof Cox, of the University of Otago, was New Zealand's representative at a meeting of the International Cancer Screening Network in Oxford, England.
One of the issues under discussion was how best to change population-based screening programmes from using faecal blood tests to one-off flexible sigmoidoscopy screening.
Prof Cox, who has undertaken considerable research on bowel cancer and was involved with the development and monitoring of the country's breast and cervical programmes, believes it would be short-sighted for New Zealand to only consider faecal occult blood tests (FOBT) for any future screening programme.
Prof Cox's attempts to have the Ministry of Health include a one-off flexible sigmoidoscopy in the pilot study due to start next year have been unsuccessful.
The ministry's commitment to FOBT seemed " unfortunately rather rigid", he said.
Health Minister Tony Ryall said the pilot was the recommendation from the Bowel Cancer Screening Taskforce, endorsed by Cancer Control NZ, and the Government was relying on their advice.
Prof Cox's calls come in the light of recent research from an 11-year large-scale United Kingdom trial where a one-off sigmoidoscopy was shown to reduce bowel cancer deaths by 31% and the incidence of the disease by 23%.
He is concerned the ministry is relying on modelling involving untested assumptions rather than actual results to support its use of an immunochemical FOBT test (iFOBT).
In a response to questions from the Otago Daily Times, Ministry of Health clinical director of the bowel cancer programme Dr Carol Atmore said the UK sigmoidoscopy study looked at how effective the test was in reducing deaths but was not designed to look at its effectiveness as a part of a population screening programme.
Prof Cox described this as a spurious argument, pointing out the long-term effectiveness of FOBT screening programmes had not been measured anywhere.
He also took issue with whether the idea of a sigmoidoscopy - a procedure which examines the rectum and lower bowel and can remove pre-cancerous polyps - might be unacceptable to people.
While having one sigmoidoscopy in your life might be unattractive for some people, having to collect faeces samples 10 times over a 20-year period, with two-yearly screening, might not suit others.
Prof Cox also rejected Dr Atmore's reference to the significant investment needed to train the workforce with the sigmoidoscopy option.
He estimated the number of colonoscopies required - a similar procedure to sigmoidoscopy but which examines the whole of the large bowel - as a result of an FOBT programme would only be slightly less than the number of sigmoidoscopies required under his proposal, based on the same number participating in the programmes.
Dr Atmore said the ministry could get under way with iFOBT screening and "start to save lives now".
The pilot would run for four years, which would give time to watch and consider the changing international picture.
Prof Cox said lives would not be saved now as the benefits from the screening would take a few years to accrue.
Flexible sigmoidoscopy would "both save more lives as fast and also prevent some bowel cancer from occurring".
It is expected that the Government will put the iFOBT pilot, which will cover a population of 60,000 aged 50 to 74, out for tender next month.