It has now emerged that in three papers reported to the National Foundation for the Deaf in 2009, Project Hearing Impairment Early Detection and Intervention (Hiedi) criticised the National Screening Unit's lack of monitoring of the newborn hearing screening programme.
The group, made up of audiologists, parents and volunteers, said implementation of a monitoring framework was urgent and could not wait until roll-out of the programme in 2010.
It asked the unit to clarify when monitoring would start.
But more than three years later, a source within the sector said a loosely implemented and fragmented national database together with limited tracking of individual screeners had led to the problem.
The source claimed DHBs had to create their own databases, some of them had never been audited, and figures from those monitored were misleading, out-of-date and not meeting targets.
The source said health officials should have known monitoring was crucial after "ethically compromised" screeners were caught in Britain.
"It was totally predictable what's happened. Maybe not the level of it, but the fact that some families would end up having kids that weren't identified as a result of the problems in this programme was inevitable."
Ministry of Health child and youth health chief adviser Dr Pat Tuohy said "a great deal of work" had occurred since the concerns were raised.
The development of a national database was being considered but was unlikely to have prevented rogue screeners, he said.
An anomaly in screening results was uncovered by the Auckland District Health Board, which alerted the ministry.
Auckland's director of child health, Dr Richard Aickin, said audiologists were not getting the expected number of potential hearing-loss cases for the DHB's population.
It found "a significant problem" with one tester, who was sacked.
"It appears that as part of their normal day-to-day work they were submitting the test results from their own ears rather than the results from a baby's ear."
Of the 2000 babies recalled, 1263 were from Auckland and Dr Aickin said only 25 per cent of parents had responded.