The Ministry of Education has appointed former Onehunga High School principal Chris Saunders as a limited statutory manager to take over governance of employment, finance, teaching, assessment and health and safety.
Principal Grant McMillan, who came to the school from Ashburton College last year, remains responsible for day-to-day management and said he had already changed all faults that NZQA found in the way NCEA was being run.
The authority found that students who tried for NCEA standards but were marked "not achieved" were then withdrawn from mark books, making it look as if they had not even tried.
It found that the school was "no longer compliant with NZQA's rules for the reporting of a Not Achieved result".
A spokeswoman said James Cook was one of just three schools where the authority found non-compliance last year, but all had been allowed to keep assessing NCEA on condition that they addressed their issues. NZQA will visit James Cook again this Friday.
The push for higher apparent pass rates also lifted real pass rates at Level 1 from 42 per cent of all Year 11 students in 2012 to 59 per cent in 2014, although that was much less dramatic than the 95 per cent figure reported for those who "participated".
But the real roll-based pass rate then fell back to 53 per cent in 2015 and just 41 per cent last year.
Real pass rates have kept rising modestly for Levels 2 and 3 in Years 12 and 13, but this is partly because of students leaving school early. This year the school has 240 students in Year 11 but only 185 in Year 12 and 163 in Year 13.
McMillan said the school had now stopped leaving some students out of NCEA.
"All students are now entered and all students have a credible programme," he said.
"My goal this year is to learn what is our normal natural rate of achievement. Then we'll set our goals and put our strategies in place."
He said the health and safety issues identified by the Education Review Office related to school trips not being signed off by the board and two teachers who had not been vetted by police to work with children because of delays in the police vetting process.
He has also referred one teacher to the Education Council, but declined to give details.
The ministry intervention is in a long tradition of interventions in South Auckland schools dating back to projects in the 1990s to improve schools in Mangere and Otara and to lift achievement at eight low-decile "AimHi" schools.
Like other schools serving low-income families, decile-1 James Cook has suffered apparent "white flight" with Europeans on its roll sliding from 14 per cent to 3 per cent since the year 2000. Europeans still made up 37 per cent of the Manurewa population in the 2013 Census.
Saunders said many European students took the train out of Manurewa to schools in higher-income areas such as One Tree Hill College.
"Once a school gets up to 97 per cent non-white it's going to be virtually impossible to turn that around in terms of the demographics," he said.
"What you can turn around is performance. That is our focus here."
NZ Council of Educational Research analyst Cathy Wylie said James Cook was a casualty of the lack of "a systematic overview of school zoning in the area".
"You need a strong South Auckland district or something that would actually take that overview of all the schools, because you can't ask individual schools to do it," she said.
"One of the solutions that they have had overseas is that they do try and draw zones to try and make a school like James Cook more viable, and not leave it up to individual schools to set their zones."
The Government has recently changed the Education Act to allow the Education Ministry to impose an enrolment scheme when a school refuses or is slow to do it, removing the need to appoint a limited statutory manager to do this.
Under state management
Schools placed under Limited Statutory Managers so far this year:
South End School, Carterton, Jan 26
Havelock School, Marlborough, Feb 9
Kaikohe West School, Northland, Feb 9
Viscount School, Mangere, March 2
Westland High School, Hokitika, March 2
Resource Teachers of Learning & Behaviour Cluster 38 based at Cromwell College, Otago, March 16
Golden Bay High School, Takaka, March 23
Hato Petera College, North Shore, March 30
Rowley Avenue School, Christchurch, June 8
Te Kura o Waikaremoana, Wairoa, June 15
James Cook High School, Manurewa, June 29
St Joseph's School, Invercargill, July 6
St Patrick's School, Nightcaps, July 6
St Teresa's School, Bluff, July 6
Muriwai School, Gisborne, July 13
Kelston Deaf Education Centre, July 13
Onepoto School, North Shore, July 20
Te Kura Kaupapa Maori o Tamarongo, Opunake, July 20
Riverslea School, Hastings, July 27
Albury School, South Canterbury, Aug 10
Hillcrest School, Pahiatua, Aug 10
