Thirty-one of that group have bowel cancer. Work is under way to determine what if any difference being missed from screening made.
Documents released to the Herald under the Official Information Act include an April 6 Ministry of Health memo to Health Minister David Clark, outlining the new address problem.
The national screening unit received two phone calls in late February from members of the public, asking why they hadn't received screening invitations. Another person had also told the DHB they hadn't been invited.
Investigation revealed a new "do not load" list problem. When the Waitematā pilot was created in 2011 it took information from the National Health Identifier (NHI) database, to build a picture of who to invite for free bowel screening.
However, this group was about a third larger than census-based population estimates, which analysts partly attributed to the inclusion of people who had moved out of the area, or were foreign visitors.
A tool was used to identify people who hadn't had contact with the health system for at least two years, and they were put on a "do not load" list, and excluded from the pilot.
Two mistakes were then made, the briefing states. During the pilot it appears the "do not load" list wasn't regularly checked for people who may have become eligible.
The second problem came after the pilot was extended to six years. A refresh allowed for newly-eligible people to be identified, such as those who had turned 50 or moved into the area.
"It appears that these people were inadvertently added to the 'do not load list' rather than invited," the briefing states.
Of the nearly 90,000 people on the "do not load" list, 9540 should have been invited for screening. Thirty-one of those people now have bowel cancer.
Another document released is a memo to the group manager of the national screening unit, the ministry team tasked with the national roll out of bowel screening. Written by the unit's manager of information, the memo partly blames the issue on a lack of resourcing.
When it was realised newly-eligible people had been mistakenly added to the "do not load" list – meaning they wouldn't get an invite – "there were limited resources available to untangle these two groups and the work was not completed".
A ministry spokeswoman said it takes full responsibility for the oversights.
"The ministry is continuing to contact those affected to apologise and invite them for screening over the coming months."
Each year more than 3000 New Zealanders are diagnosed with bowel cancer and more than 1200 die from it. There can be no warning signs cancer is developing, and early detection is critical.
A bowel screening pilot started in Waitematā DHB in 2011 and detected cancer in 375 people, leading the previous Government to commit to national screening.
Hutt Valley and Wairarapa health boards began screening in July last year and Waitematā moved from its pilot to the national programme in January. Otago and Southland DHBs joined last month.
Screening will be offered every two years to men and women aged 60 to 74. Once fully implemented it's expected to detect 500-700 cancers a year.
The "do not load" problem was announced by the ministry shortly after the Herald revealed another problem with invitations had excluded 333 New Zealanders.
Waitematā DHB has made clear the address register used was the ministry's responsibility, and limitations were repeatedly raised by the DHB.
Clark had already ordered an independent review of the national screening programme, after another problem saw the ministry last year write to 2500 Waitematā residents who had been missed.
As part of yesterday's Budget, Clark announced $67.1m of operating funding to roll out screening to a further five DHBs over four years. The money will also fund a national coordination centre, four bowel screening regional centres, and an IT programme to help avoid the type of problems that beset the Waitemata pilot.
• People with questions about their eligibility for screening can visit www.timetoscreen.nz or call 0800 924 432
