It sparked street protests and legal action as schools and communities fought to save their schools, which they argued had been the centre of their communities during the tumultuous 2010/11 Canterbury earthquake sequence.
The report recommends that the ministry publicly apologise to schools and communities through the local press, and work with education sector groups to develop a stronger and more effective engagement process around school closures and mergers.
"Disclosure acknowledges that ministry staff faced unprecedented challenges in the Canterbury schools reorganisation," said Chief Ombudsman Peter Boshier.
"In dealing with the aftermath of one of New Zealand's worst natural disasters, the ministry was hindered by the absence of any established process for even small-scale school reorganisations.
"Staff lacked institutional systems or procedures that could have resulted in a much better experience for communities", the Chief Ombudsman said.
There was a fundamental lack of transparency in the ministry's approach of running two parallel processes - one visible to the community, the other not.
"Essentially, while schools and communities were engaging in what they thought was a genuine discussion about broad future visions for schooling in Canterbury, the ministry was progressing a business case with detailed plans for individual schools," Boshier said.
"When these plans were announced to schools on 13 September 2012, the announcement itself was poorly handled by the ministry, with inaccurate and insufficient information provided. Schools felt blindsided by the detailed proposals, and the statutory consultation process from there was mired in mistrust and defensiveness."
Disclosure concludes with the recommendations that the ministry publish a written apology in the Christchurch Press to the schools and communities affected; and work with education leaders to develop a strong, effective process for future engagement on school closures and mergers.
"I commend the Ministry for accepting my recommendations," Boshier said.
"I welcome this as a priority for the ministry, and I will continue to monitor progress."
The ministry today apologised for "failures during our early engagement" with the Christchurch community over school closures and mergers following the Canterbury earthquakes.
"We didn't provide the information people needed and as a result, they were shocked and surprised by our announcement on 13 September 2012 about proposed closures and mergers," chief executive Iona Holsted said.
"They deserved better. We let them down and we are sorry. We know this undermined trust and confidence in us, as the Ombudsman's school closures report confirms.
"We should have provided better information in the lead-up to the Lincoln announcement about how the budget and decision-making process to develop initial proposals worked. The way we informed schools of those proposals was poorly handled and the information we provided then and in the immediate aftermath was not good enough.
"We didn't set out to mislead or to keep people in the dark, but the result was that we weren't as transparent as we should have been.
"The scale of the damage and disruption caused to schools meant this was an extraordinary situation - we'd never encountered anything like it before. As the Ombudsman says it was a 'Herculean task of educational renewal in a post-disaster environment'."
While intentions were good, Holsted admits they should have done a better job.
Today, she apologised for any distress that it caused to parents, students, teachers, leaders and their communities.
Holsted said a lot of work has been done since the beginning of 2013 to provide the right information to the schooling sector in Christchurch and to "put things right".
"We changed our approach and the improvements we made along the way have become part of our standard approach to school closures and mergers," she said.
"We now engage with schools earlier in the process and provide them with the information they need as early as we can.
"We have agreed to both of the Ombudsman's recommendations. We will work with the sector to revisit the closure and merger guidelines that we developed with them in 2013 to ensure they provide sufficient clarity around our policy and practice and reflect good consultation practice."
Deputy State Services Commissioner Debbie Power today said she supported the steps the Education Ministry has taken to put things right.
"I commend them for recognising they got their processes wrong, apologising for it and making sure it won't happen again."
A synopsis and the full report are available at www.ombudsman.parliament.nz