The suggestion was endorsed by the boy's grieving father Dr Anjan Banerjee who said the stall design provided children with another way out of a toilet cubicle should they become trapped.
But today the ministry's deputy secretary Jerome Sheppard said it would look at design guidance but all buildings must comply with the Building Code.
The ministry would follow the coroner's suggestion to provide the findings to all schools but it would strongly recommend school boards follow ministry design guidance for toilets.
His call for changes to school toilet doors and window latches were inconsistent with the code in many circumstances.
"The coroner has suggested that stall-type doors and window latches in toilets should be removed.
"However clause F4 of the code, for example, contains technical provisions relating to barriers on windows where children could fall from a height of a metre or greater," said Sheppard.
"Requiring latches to be removed from toilet windows may therefore be inconsistent with the code in many circumstances. "
The code also prohibited stall-type doors in unisex toilets for privacy reasons.
"The Ministry's current design guidance, which we strongly recommend that boards follow, recognises the benefits of schools using self-contained cubicles - including the minimisation of anti-social behaviour and because they can be used as unisex toilets," he said.
The ministry acknowledged the difficult time the Banerjee family had gone through as well as the staff and children at Taradale School.
In his findings released today Scott said the school caretaker was in the middle of urgent repairs to fix the door handle and had left for three to five minutes to get tools.
However, Scott said he must have been longer than that, with no real urgency demonstrated to get the job done.
He said access to the bathroom was not blocked, no warning signs, cones or tape were in place, although they were available.
Critically, the manually operated catch was off the lock in the door.
Scott said the caretaker should have spotted the risks. Two other children had previously been trapped in the toilet, including the principal's own child.
Scott said it was "also foreseeable that Aryan would attempt to escape via the window".
"On the balance of probabilities, [the caretaker] should have foreseen as a consequence what actually happened."
The simplest and most obvious way of preventing the toilet from being used was to close the door. "That is all that is needed to have been done," he said.
Scott said the caretaker had been significantly affected by what happened and was regarded as competent by the principal.
The man, who has name suppression, is still on school staff and has not faced disciplinary action.
Police and Worksafe have not laid any charges.
The coroner did not make any recommendations, saying they may be unworkable.
Instead, he has suggested that all school toilets should have stall-type doors, with a gap at the bottom, and windows that can fully open, in the hope of avoiding a repeat.
He asked the Education Ministry to distribute his findings to every school in the country.
Dr Anjan Banerjee told Radio New Zealand the coroner's report went a long way to vindicating his son for taking the action he took.
"The Worksafe report left the blame almost entirely on Aryan and that did not sit well with me - it wasn't the right decision in my view - so having the coroner's inquest and going through the detail allowed us to vindictate him."
However, there was still an enormous shortcoming in the law that meant schools did not have to warn children of potential problems.
"I still to this day cannot understand why there is no kind of health and safety requirement for out-of-order signs on toilet doors in children's areas in schools."
He said the foreseeability was an important aspect in his son's death.
"That's why we have health and safety rules. In just about every other aspect of our life we have rules that say if the floor is wet you put up a sign, if the toilet's not useable or the door's not safe you put up a sign. Not putting up any kind of warnings or making it so that nobody could use the toilet because you could not foresee any kind of injury occuring was what I thought was the important thing there. He didn't put up any signs and Aryan got hurt."
Banerjee welcomed the coroner's suggestion to use stall-style doors in school toilet cubicles. This provided an emergency exit if something led to pupils being trapped.
At the time of the inquiry, the ministry permitted full doors on toilets and these were still being used in the primary school where his son had his dreadful accident.
"I would argue that they should all be stall doors. The ministry this year put out instructions that all toilets should have full doors and that, in light of what happened to Aryan, just beggared belief, " said Banerjee.
He said the latest report brought everything about his son's death to the fore and brought back very difficult emotions.
"It's still too raw though. It's only a year and few months since he died and it takes a very long time to come to terms with these things."
