Associate Prof Brian Cox, of the University of Otago, said he feared the faecal occult blood test (FOBT) method being trialled in Waitemata had become a ''juggernaut''.
The Government is under pressure to confirm a bowel screening programme, and consultation with the health sector starts today.
New Zealand's incidence of bowel cancer is among the highest in the world, and a low detection rate and lack of early treatment was highlighted this week in the Presentation, Investigation, Pathways, Evaluation and Treatment (Piper) project.
A pilot scheme running at Waitemata since 2011 is using FOBT, which involves self-testing kits and colonoscopies for patients who return worrying results.
Prof Cox said flexible sigmoidoscopy (FS) was a better screening method and would prevent more deaths.
It involved an endoscopic examination and far fewer colonoscopies.
For years officials have cited increased demand for colonoscopy as a reason to delay implementation of a screening programme in New Zealand.
Adopting FS would eliminate that problem, Prof Cox said.
It would increase demand for colonoscopies by just 2% per year (10% over five years) and ''I'm sure the system can manage that''.
Prof Cox said he feared it would be difficult to shift the mindset away from FOBT.
''There seems to be some very fixed viewpoints about the value of FOBT and that that's the way we should go, yet it's rather outdated.
''It's become a juggernaut.
''Unfortunately, that's probably not the best approach for New Zealand at all,'' Prof Cox said.
The United Kingdom started with an FOBT programme, but was now working out how to run it alongside an FS programme.
''Once you go with FOBT it gets very hard to go to the better screening [FS].''
In a recent presentation to a conference in Auckland, Prof Cox presented a paper showing cost savings from FS and FOBT.
Annual savings from FS were $19.58 million through reduced cancer treatment, against a $3.6 million saving from FOBT (once the programmes had been running for about 15 years).
''Flexible sigmoidoscopy reduces incidence of the disease considerably. Therefore, you save on the treatment costs of those individuals.''
Health Minister Dr Jonathan Coleman's office said it was too early to talk about screening methods.
Earlier this month, he said he expected to take a business case to Cabinet by the end of the year for a national screening programme, but would consult the sector first.
Ministry of Health bowel and prostate cancer programmes manager Mhairi Porteous said the consultation process was starting with a meeting hosted by the ministry today in Wellington.
''The ministry intends to follow this up with regional meetings with providers, where more detailed and focused discussions will take place.''
