Mr Clarke said no threats were made but he was uncomfortable with the questions he was asked. He declined to say what those parents had said.
Mr Clarke then contacted the four-year-old boy's parents to ask them to take home the boy's two siblings, who currently attend the primary school.
"I made the professional call that in the environment of uncertainty, possibly ignorance, I'd go and approach the family and say, 'In the physical and emotional interests and safety of your children, would you mind taking them for a few days'," he said.
"I went and saw the family straight away, and they were happy with my explanation until I could have further conversations with some people."
The boy's siblings were taken home that day.
Mr Clarke had since spoken to the two parents and was satisfied the situation was cleared up.
The boy's siblings returned to school as usual today.
Mr Clarke said he yesterday held a meeting with three generations of the boy's family, Ministry of Education officials, health officials and a delegation from the New Zealand Aids Foundation.
The school called the meeting to develop a care plan for when the boy starts school in July.
"I was happy to have everybody in there to say, 'The experience you got over there [at the daycare centre] is not what you're going to get here'," Mr Clarke said.
A Ministry of Education spokesman told the Northern Advocate the principal was "reminded" that all primary and secondary schools were required to admit pupils regardless of their medical condition unless a notifiable disease had been confirmed.
"Families of children with HIV are not required to disclose to schools and Early Childhood Education services of their diagnosis as there is no risk posed to other children. HIV is not a notifiable disease," the spokesman said.
Mr Clarke said the school was not reminded of its legal requirements and did not need to be.
"I had nobody come to me from the ministry to remind me of my legal requirements because I know the legal requirements."
The boy had been attending the Mokopuna childcare centre for four months before the centre learned he had HIV and asked his mother to keep him at home until a care plan was completed.
Centre management said the boy had not been excluded or expelled. He was welcome to return to the centre once the plan had been created to address his medical needs, centre operator He Puna Marama Trust chief executive Raewyn Tipene said.
However, the Aids Foundation has disputed this, labelling the care plan a strategy to shut out the boy.
The trust is now preparing to take legal action over "untrue" claims made by the Aids Foundation, which Ms Tipene said were an attempt to boost its funding.
- Additional reporting Northern Advocate
