Girls and young women aged between 10 and 19 raised funds. The money was deposited into a Miss Junior New Zealand bank account or given in cash to organiser Collette Lochore.
Lochore, a former Miss World New Zealand winner and a MasterChef contestant, set up the pageant in 2012.
The deadline for donations to be deposited was the week before the show's final, held at Avondale College on April 12.
An email sent from Miss Junior New Zealand administration to all the families involved on April 28 stated: "Charity cheques will be sent out via courier track and trace as soon as possible to your selected charity."
Lochore would not discuss the matter yesterday.
"I don't wish to talk to you guys.
"If they've [parents] got concerns and they want to go to the Herald about it they're most welcome to and I've got absolutely nothing to hide about it ... I'm not fussed by it, so that's cool."
Asked when the charities would get the money, Lochore hung up. She later sent a text message saying she was "not sure what the concern is ... it's all under control".
Parents involved with last year's pageant were also concerned what happened to money their daughters raised for charity.
They say they gave money directly to Lochore, on the understanding she would pass it to the appropriate charity.
An information pack from last year claimed Miss Junior New Zealand worked "hand in hand with Variety, the Children's Charity".
It also said: "We always endeavour to select charities where 100 per cent of our donation goes to the children." Variety said it knew of Miss Junior New Zealand but could find no record of receiving any money from the organisation.
Charity work is a key component of the Miss Junior New Zealand competition and makes up a large percentage of the judging score.
The Facebook page for the pageant contained posts relating to contestants' charity work.
Fundraising ventures included movie nights, cake sales and raffles.
Some concerned parents said their daughters put in time and effort to fundraise for their charity.
The pageant has been in the spotlight before, about concerns over the youth of the contestants and broken promises.