A mother has been convicted for keeping her children out of class after using medical certificates to claim they were constant victims of poor health - except for the days when there were fun activities at school.

In a rare prosecution, the school forced the mother into a courtroom.

It was the only case of its sort last year - and one of only 43 prosecutions in the last eight years. Around 800,000 children currently attend primary school.

The mother had denied the charges, saying her children - aged under 10 - were actually sick.

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Judge Geoff Rea convicted her but ordered no punishment, instead offering a warning that if she would not fulfil responsibilities as a parent then "forces beyond me will undoubtedly take charge and that may not be a happy outcome".

"It is a sad day indeed when a school has to get to this stage to try and enforce your responsibilities for your own two children."

The mother, whose name is suppressed to protect her children, was brought to court as a "last resort" by a Hawke's Bay school which had struggled for years to get her kids into the classroom.

The court ruling on the case shows one of the children only turned up for school 50 per cent of the time in the first term of 2017 while the other was present only 75 per cent of the time.

The national average for their age group was 92-93 per cent.

Records showed similar poor attendance during the prior two years.

The actual non-attendance figure would have been even higher, according to court papers, but for the string of medical certificates produced to justify absences.

Rea said huge effort had gone into trying to get the mother to bring her children to school more often.

It involved health authorities, Oranga Tamariki and family assistance specialists but nothing made a difference.

After two years, the school brought the mother to court "as the only way of bringing home … that she had fallen woefully short of her obligations as a parent and that was impacting adversely" on the children.

Rea said he was concerned over the medical certificates presented to the school for times the children had been absent.

"There are various examples of them, but they really only said that the child was unable to attend school because of illness without providing any reason at all as to why that was the case or why the particular periods of time that are nominated should be necessary."

Rea said the situation was "increasingly concerning" that the school contacted the medical provider and raised concerns.

The medical certificates then "change format" and instead said the child had seen the doctor and was "unable to attend school yesterday" but would be present that day.

"With respect, that is not an adequate medical certificate dealing with the absence of the child the day before based on what the mother has said."

Then medical certificates changed again, saying only that the child had seen a doctor and "blandly asserting that the child was unable to attend school over a four day period because of illness as reported by mum".

He said the school would have found it "extraordinarily frustrating" but the "headmaster felt obliged to accept it as a valid medical certificate".

Even though forced to accept the medical certificate, the principal then would note "a child being absent on one day, competing in the swimming sports the next, and then being absent the third day".

Rea said it was a feature that "special days" at school saw both children attend.

Meanwhile, the mother - who had "cut herself off from a rational view" - would claim the illness suffered by the child was Intermittent.

Rea told the mother "you will know your children better than anyone" but said she needed to give the children the same opportunities at school others had.

He said "the world is becoming more and more competitive and every piece of education that they can get will assist them into the future".

NZ Principals' Federation president Whetu Cormick told the Herald there was little schools could do to challenge medical certificates.

"If a parent produces a medical certificate from a doctor, the school is not in a position to question it."

Cormick said schools would rather the Ministry of Education took prosecutions and sought greater support.

Royal NZ College of General Practioners president Dr Tim Malloy said examinations of children were particularly difficult because they generally saw the parent involved as a driving figure.

"The doctor-patient relationship depends entirely on trust. We are asked to make decisions on information provided by patients."

Confidentiality was also a factor, with medical certificates simply explaining a person was unable to work - or attend school - but offering no further detail without the patient's consent.

He said doctors were not able to produce "sick notes" for previous absences - it could only be for present or anticipated absences.

Ministry of Education deputy secretary Katrina Casey said there was a maximum $3000 fine.

"It's really important that children go to school every day if they are to achieve at school."

She said the main responsibility was with parents but schools had the power to prosecute which was used as a "last resort".

Casey said prosecution was only considered in cases where absence was unjustified, persistent and with parents' permission or ambivalence.

She said the school took charge of the prosecution because of its specific knowledge and was backed up by the ministry.