Of the 137 English-medium schools with year 1-8 pupils in the Otago region, 37 submitted their charters in August without setting targets in relation to National Standards, figures released by the ministry under the Official Information Act (1982) show.
However, as at September 22, only two of those charters still did not contain the targets.
The standards regime has come under intense fire from teachers, parents and academics concerned at the speed of its implementation and the effects it could have on children who are falling behind.
The Pembroke School board of trustees and its principal, Brent Godfery, are among the more outspoken ones but, like many others in Otago, they are now working to make their charter meet the criteria.
Mr Godfery said they had to submit to the ministry's pressure because it was threatening to appoint a statutory manager for the school.
"The appointment of a statutory manager must be paid for from school funds.
"We have made our point, but we do not want our students to suffer because funds for learning are diverted by the ministry to support the introduction of National Standards. I must say, we do feel like we've been bullied into submission."
Mr Godfery said he and the board still opposed the National Standards, but would now have to find another way to protest.
Otago Primary Principals' Association president Bernadette Newlands said schools had a choice to send in charters with targets that reflected the needs of their pupils. In some cases these mentioned National Standards, and in other cases they did not.
"In some cases, it would have been a deliberate stand against National Standards but in others, they were just setting targets as they always had, based on the needs of their students."
Mrs Newlands said schools were trying to comply with the law and they would be better served if the ministry spent more time resourcing and supporting them rather than "chasing up non-compliant wording".
Education, Curriculum and Performance acting senior manager Don Couling said this was the first year schools had had to set National Standards targets in their charters, and there were several reasons a charter might not contain them.
"Some schools have required additional assistance to meet these requirements and have subsequently submitted compliant charters.
"The ministry is working closely with schools unable, or unwilling, to set targets in relation to National Standards, to ensure their charters meet the requirements of the Education Act 1989."
