ERO national evaluation services manager Diana Anderson said there was a small group of schools philosophically opposed to the standards, but the number had fallen since the last report.
An increasing number of schools were now using standards more and more effectively, she said.
"It's gradually becoming more and more business-as-usual for more and more schools. Schools are obviously on a continuum, and we have a small group of schools still who are not doing well with the national standards.
"But that group size has got smaller - particularly the ones that are in direct opposition is a very small number now."
Ms Anderson said in the schools that were struggling to implement the standards, there were often governance issues that distracted from the primary business of student achievement.
Labour education spokeswoman Nanaia Mahuta said she was not aware of a school that fully endorsed national standards.
"They've said it's there and they're going to implement it, but whether it's an accurate measure of children's learning and progress, the strong view that I'm hearing from teachers and principals is that it is not," she told APNZ.
Ms Mahuta said she did not buy that schools had such severe governance issues that they were not meeting achievement levels.
A spokeswoman for Education Minister Hekia Parata said the number of schools protesting national standards, by refusing to put targets into their charters, was now down to one.
Ms Parata said the ERO report referred to was from last year, and it was understood the last school not to include national standards in its charter would comply this week.