This week, Social Development Minister Paula Bennett defended CYF when responding to questions from the Herald on Sunday.
"While a statistical reporting error is certainly not ideal, I'm pleased the department picked it up, was publicly upfront about it and quickly moved to fix the issue," she said.
She was adamant the prolonged under-reporting had not jeopardised the well-being of children at risk.
"This statistical error has no impact on the way we work with children, nor does it impact staffing and resourcing," she said.
The Herald on Sunday has discovered Bennett's flagship White Paper on Vulnerable Children was compromised, as were the Ministry's 2011/12 and 2012/13 annual plans.
Those documents and answers to parliamentary questions, an Earthquake Recovery Authority report on neglect in post-quake Christchurch and research by the Child Poverty Action Group now contain inaccuracies due to a computer glitch.
Since a 2011 computer upgrade, regular snapshots of data taken from CYF's main computer system have not captured all the information available. The system was designed to pick up data for each month including information entered a month and two days after the month ended. Instead, the snapshot cut off two days after the month ended, meaning all late-entered data was left out.
The ministry believes that the error doesn't contradict any statistical trends, but CYF's statistics have been removed from the website while they are recalculated and checked.
Ministry chief executive Brendan Boyle said data from 2011 onwards was affected. "The initial review of data shows a margin of error mainly around 2 to 3 per cent, up to 8 per cent."
Donna Wynd of Child Poverty Action said: "All they're doing is keeping a tally. How you can make such a simple error?"
Wynd said abuse notifications data tended to be volatile, affected by high-profile child abuse cases and advertising campaigns encouraging public vigilance.
Knowing the problem stemmed from a computer upgrade was far from reassuring.
"They now want to upgrade their computers so they can share information. Can we trust them?"
A Christchurch Earthquake Recovery Authority spokeswoman said the error would have had no effect on its work of prioritising children and parents as a target group for psychosocial services.