"Programmes such as this often create debate and strong opinion," the letter said.
"The board of trustees believes that our school values are central to creating a positive learning environment for all students. We feel that continuing to offer the CRE programme, albeit in a different time slot, while also taking the time to actively consider the diverse views on this issue, is consistent with those values."
Everyone at the school was "very happy" with the decision, said Maheen Mudannayake, who made an official complaint to St Heliers School.
It was a "win, win" situation, he said, with parents who wanted their children to attend the Christian religion classes still able to send them to the after-school lessons, and parents who didn't able to "not worry about it".
"I saw one of the parents this morning and she said, 'oh I'm so relieved'," Mr Mudannayake, who is a Buddhist, said.
"What's good from my point of view is that the school listened and acted, it's just a shame they didn't act when we were bringing this up in 2011.
"But it just took one person to stand up and then basically everyone came out of the woodwork and things moved [quickly].
"All of a sudden with Roy [Warren, a fellow-parent at the school] coming out it's gathered so much momentum," he said, adding it was less than a month since Mr Warren first spoke to media about the issue.
"That's just unbelievable."
St Heliers School principal Craig McCarthny said it had been "quite a complex issue'', and a number of factors had led to the decision. He said the complaints to the Human Rights Commission were just one factor.
He said the main reason was the increasing demand on teachers to meet the current curriculum within a stretched school timetable.
"That had been on our minds for some time now and then when the issue about CRE came up ... I suppose it just heightened our awareness,'' he said.
"With all the different opinions it seemed a good time then to talk about that side of things, and I believe that the board has come up with a very good solution.''
He said parents at the school had been very supportive over an issue that ``creates a lot of opinion and debate''.
"People can have very strong views on it [teaching religion], so sometimes it's difficult to come up with a solution that suits all,'' he said.
"But we think, in this case, it's a good outcome for everybody.''
The Secular Education Network, which has been supporting them in their fight, wanted Mr Mudannayake, Mr Warren and Ms Muirhead to talk to other parents in other schools about the process of challenging religious education, he said.
"It's not just one school, there are other schools that are having problems as well."
Mr Mudannayake said the model St Heliers School had chosen was "quite good".
"It's outside school hours, it's opt-in, it's just like an extra curricular activity now like music or sport, I think that's a good model for all of New Zealand," he said.
"In theory you could have other religious groups coming in and running education classes too, because it opens it up now."
Mr Warren said he was pleased with the result, and he hoped other schools would follow suit.
"I think there's a pattern that may well continue, not just with other schools in our local area which may run the programme, but hopefully in the wider New Zealand community," he told Radio New Zealand.
"I think the schools that continue to run programmes like this need to take notice and think about what they're doing."
Mr Warren earlier said he had been overwhelmed by the support shown by other parents of the school, and hoped the result would give courage to parents in schools throughout the country to challenge such programmes.
The Secular Education Network said it was "over the moon".
Public relations officer David Hines said he was not surprised with the result as there were early signs the school was taking the complaints seriously, and the protesters were a "very persuasive group".
The Christian classes were taught to Year 1 and 2 pupils for three terms and involved storytelling, songs, drama and crafts.
Children who opted out were sent to other classrooms to work.
Mr Warren and another parent Melissa Muirhead both chose to keep their children in the classes because they did not want them to feel isolated from their classmates.
The complaints to the HRC claimed the classes were discriminatory by excluding children from their friends on the basis of religious belief for the period of the class, making the children feel ostracised and different.
The HRC complaint had gone to mediation, and a decision was not expected for some time.
