The following year a survey estimated more than 3000 leaky buildings - 18 per cent of all school property by area - needed fixing at a cost of $1.4 billion. The estimate was later revised down to 2500 buildings and a $1.1b price tag.
The ministry has admitted that progress so far has been slow, with only about 500 buildings repaired since work began in 2011 at a cost of $425m - an average cost of $850,000 per building (including some upgrades done at the same time).
Head of Education Infrastructure Service Kim Shannon told the Herald this week that further investigation this year had shown just over 1000 buildings still needed weathertightness repairs. The cost was still unknown but the work was expected to be quicker and cheaper than before.
Shannon said a comprehensive review of the work completed over the past six years showed that in many cases most of the building work and associated spending was not well targeted.
"This building work usually involved a full "re-roof" or "re-clad" that often led to unnecessary disruption to schools, higher costs, and delays in addressing proven cases of failure and damage."
She said some cases would probably still require this approach.
"However, based on experience, we also anticipate many instances where less remediation will be required, and may well be adequately addressed under maintenance. This means we are better placed to respond to schools based on how critical their needs are, so good progress towards remediating weathertightness issues can be made."
Building surveyor and mediator William Hursthouse has criticised the new policy as short-sighted.
In an opinion piece written for the Herald, Hursthouse said targeted repairs could work in the short term but would fail sooner or later without a thorough follow-up monitoring regime, which was not required by law.
"The Ministry of Education will eventually discover what most experienced building surveyors already know; that for the majority of leaky buildings with... untreated framing and direct fixed cladding, recladding remains the most sensible and cost-effective option.
"Doing targeted repairs on buildings with such fundamental system flaws is like putting a tourniquet on a gaping thigh wound - it will work for a while, hopefully until the patient gets to hospital, but no one expects the leg to survive for long if that is the only treatment given."
Hursthouse added in an interview that "it will all end in tears" if targeted repairs on school buildings went ahead without a stringent maintenance and monitoring programme.
He was also concerned about the risk of legal action because the law currently made any builder who carried out a partial repair responsible for the weathertightness of the whole building.
"At the moment targeted repairs are far too risky because of the standard that the Building Act requires... People get sued."
Secondary Principals Association president Mike Williams said some early large-scale repairs of school buildings had turned out to be unnecessary but he was not sure whether the ministry's new targeted repairs policy would work.
"The track record's not great. The bureaucracy tends to confuse what happens at times."
Williams said some buildings had very minor problems, which could be fixed with spot repairs, but others required major work which was taking years.
His own school, Pakuranga College, had fixed its major leaky building problems but still had minor work to do.
Leaky schools
Number of buildings repaired: 500
Cost so far: $425 million
Average cost per building: $850,000
Number of buildings left to repair: 1000
Estimated cost: Unknown
Source: Ministry of Education