"The system was never going to accommodate wherever there was a judgement [to be made]."
His staff had a "pretty good handle", but there were inconsistencies between schools as well as teachers.
He received occasional feedback from parents, concerned when their child ranked lower than expected.
Mr Soar said parents should focus on their child's achievements in school reports before taking into account national standards data.
"To be able to show that they're making progress is probably more important. There's always going to be a percentage that are above, a percentage that are below and a percentage that are average," he said.
"It could lift ... but it's always going to be a reality of society."
New Zealand Educational Institute national president Judith Nowotarski said the report confirmed what teachers had been saying since day one.
"It's deeply flawed and unhelpful. Data about children's progress should never be used to compare schools because children learn at different rates and in different ways."
The "unfair system" should be scrapped completely, she said.
"We don't want to see our kids labelled as failures because they haven't met a set target in an aspect of the curriculum."
It was an insult to blame teachers for the inconsistencies, she said.
New Zealand Principals' Federation president Phil Harding said the report showed the national standards assessment system was shonky and unreliable.
"We have been saying the data is not valid and reliable for the last four years, so it is a great vindication to have that put in black and white and especially to realise that if the overall teacher judgments are wrong, so are all the deductions that flow from that," Mr Harding said.
However, Education Minister Hekia Parata said it was just the second year of reporting and the system needed time to improve.
"National standards will get better and better as has happened with NCEA, as has happened with delivering the curriculum."
The standards had never replaced conversations parents could have with their children's teachers about their child's progress, Ms Parata said.