The investigation would focus on whether the consultation processes operate in a manner that adequately ensure fair and meaningful participation by affected parties and, if they do not, how they could be improved.
The Education Act requires the minister to consult prior to closing or merging schools and the ministry plays a key role in assisting the minister with those consultations.
The Ombudsmen Act did not provide scope for the Ombudsman to investigate the actions of the minister, but would look at the role the ministry plays in assisting the minister.
Ms Parata said in Parliament she had confidence in the ministry and said they had worked hard to get closures and mergers right.
"We have resourced this process exceptionally well, we have doubled the length of time available we've made all information available as soon as we've been able to, we've responded to all requests for meetings, I have visited every school twice, we've provided an 0800 line, we've provided a website - I think we have done a pretty good job, but we can always do better."
Mr Donnelly said there had been an increase in complaints about the Education Ministry in the past two years.
Labour's education spokesman Chris Hipkins said the investigation was likely to show what people in Christchurch already knew - "that the information was faulty, that the process was faulty and that decisions the minister made as a result of that were very likely to be challenged."
He described the process as a "train wreck" and said it was a "slap in the face" for Ms Parata.
Green's Christchurch education renewal spokeswoman Catherine Delahunty said the investigation was too late for some schools.
"It's completely unacceptable that, this far into the so-called consultation over school closures, schools are still waiting for evidence to support the fundamental premise of the Government's decisions," Ms Delahunty said.
Three Christchurch intermediate schools said in February Ms Parata broke promises to them that they would remain open until the end of 2014 to allow newly enrolled students to complete their intermediate education in one place.
Ms Parata denied in Parliament she ever made a promise to the three schools, despite parents, teachers and principals saying they were assured by her during consultation meetings.
It is expected the investigation will be completed in the second half of this year.
