Dr Stein, a gastroenterologist at Hutt Valley District Health Board, is co-chairman of Crohn's and Colitis New Zealand, which advocates for patients with those conditions.
This week, the Otago Daily Times highlighted the plight of Dunedin woman Gaynor Bungard, who was promised major bowel surgery for ulcerative colitis a year ago.
She has no date for surgery, and the Southern District Health Board says other patients have a greater need.
Mrs Bungard is unable to leave her house without fasting because of the condition.
She has had several trips to the emergency department when her symptoms become acute.
Increasingly, the need to meet targets for prompt treatment for cancer patients is pressuring DHBs to drop other cases.
Dr Stein said he was a ''strong supporter'' of bowel screening, but was concerned the system did not have the resources to cope.
''We're all worried about the bowel screening, to be honest.''
There was already significant pressure on operating theatres and intensive care units, forcing doctors to become ''advocates'' for patients.
''At my hospital we're just starting... we're one of the pilot hospitals [for bowel screening]. But we don't have the capacity to handle the extra colonoscopies that are going to come through. I don't know what we're going to do.''
''We have people with inflammatory bowel disease that need colonoscopies [too].''
The Government says it is increasing funding for colonoscopies to meet the extra demand.
Health Minister Jonathan Coleman said last month the Government had spent $77.8 million on the screening programme to date, and a further $19 million on colonoscopy services.
