"It was only when a number of things came together at the same point we thought, 'something's wrong here'," he said.
"The shock when it was first realised was quite significant."
The principal said the amount allegedly stolen was clearly significant but had gone unnoticed during the day-to-day running of the school.
He accepted the school's name would probably come out at some stage when suppression orders lapsed and insisted they had nothing to hide.
Regrettably, the school had not been able to inform parents because of the restrictions on publication but he said that would be done as soon as was legally possible.
The woman, who is on bail, could face up to seven years jail if found guilty.
She will be back in court again later this month when she is expected to enter a plea to the charge.
PREVIOUSLY
May 2014 - Mayfield Primary School principal Colleen Gray is sentenced to one year's home detention and 150 hours community work after siphoning more than $30,000 from a decile one school. Her husband, Bruce, is also sentenced to 10 months home detention.
Nov 2014 - Sayonara Fa'amausili is sentenced to 40 hours of community work for stealing $89,068 from the pre-school where she was centre manager. The Teachers Council heard she had become "besotted" with a man and the money funded his drinking and gambling addiction.
Jan 2016 - Tessa Fiona Grant pleads guilty to stealing $795,000 while working as the commercial manager at Waikato Diocesan School for Girls. She used fake invoices to swindle the cash over just nine months and spent it on an equestrian centre in Horotiu, as well as a horse and jewellery.