The Education Review Office says only 22% of the schools it visited last year were working well with the national standards in reading, writing and maths.
The primary school union says that is because most schools have little faith in the standards.
The ERO says a little over half of the 439 schools it assessed were still developing a way to work with the standards - a group that include schools only just starting to consider the benchmarks.
A further 84 were even further behind, often because they were poorly run.
The primary school union, the Educational Institute, says schools would be doing better if the standards were actually useful.
It says schools are measuring children's achievement using the best tests and benchmarks available - and those are not the standards.
The Principals Federation says it will take several years before schools get to grips with the standards.