One school had begun a series of uninterrupted sessions in literacy and numeracy from 9am-11am every day.
Other issues were teachers feeling overwhelmed and overloaded with work and students feeling bad about not meeting standards - despite making progress.
"Teachers are putting too much time and effort into the overall teacher-judgments, which lie at the heart of national standards," Professor Thrupp said.
"There's so many different bits of assessment and they spend a lot of time checking, moderating and working to get it right. So there's an opportunity cost - they could be putting their time into other things; like teaching children."
The report showed that out of the six schools surveyed, two had refrained from using the four-point grade system - well below, low, at or above national standards - because they did not want to label its pupils. They only changed their stance after the Ministry of Education enforced it.
Another school who was not using the "well below" grade had also just changed last year after being asked by the ministry.
Professor Thrupp said there was a need for immediate change in the policy to help students and teachers.
"National Standards assessment is becoming too dominant and taking over in the schools too much. There's a need to change policy to free teachers up ... so they're not so preoccupied with the national standards and the whole business of making the judgment on that very simple and crude scale - well below, below, at or above."
NZ Principals' Federation president Phil Harding said: "[The report is] confirmation [that] all the dire warnings and the negative consequences of this national standards policy are coming true.
"The only fix is a dramatic re-think of the policy. We've now got a high-stakes model ... this is damaging the New Zealand education system and it's no better than a national test."
A spokeswoman for Minister of Education Hekia Parata said she would not be able to comment as she had not read the report.
National Standards
• Introduced in 2010.
• Set standard that children in primary and intermediate schools are expected to achieve in reading, writing and maths.
• Includes a four-point grade system reporting whether a student is well below, below, at or above the expected national standard for a particular category.
• Has been controversial among teachers who claim that it limits the way students are taught.