The head of one of two primary schools at the bottom in this year's government league tables has criticised them as "misleading".
It is claimed the tables do not "reflect a school's strengths"
Cecelia Davies, headteacher at Moor Nook Community Primary in Lancashire, has called for the way the tables are compiled to be reformed.
She claims the school, in Preston, was poorly placed because the number of pupils with special educational needs (SEN) was not considered
Another school, in Nottinghamshire, has also criticised compilation methods saying its placing at the bottom of another table was dictated by poor results in just one subject.
In the tables, published on Thursday, Moor Nook Community Primary School in Preston came bottom of the table showing the proportion of 11-year-olds reaching government standards in English, maths and science.
Manton Primary School in Worksop was at the foot of the so-called "value-added" table that shows whether or not schools helped their children to improve been the ages of seven and 11.
At Moor Nook, in tests used to compile the tables,14% of 11 year olds reached the government's required standard in maths, 20% in English and 31% in science.
The national average is 75% for English, 73% for maths and 87% for science.
However, head teacher Cecilia Davies said 25 out of the 35 children who took the tests - 71% of the group - had SEN, which had distorted its placing.
"It doesn't tell you anything about the true performance of the school," she said.
Education watchdog Ofsted had praised the school for its teaching and good management, she added.
League tables "fail to show the strengths of the school and are misleading because some people will read them and think this isn't a good school," said Mrs Davies.
"If they are here to stay, they have to be reformed."
In the new "value added" tables, based around 100, Moor Nook's score of 98.5 put it in the lower quarter of results - but nowhere near the bottom.
With a score of 95.2, however, Manton school had the lowest score in the country.
Head teacher Bill Ball said: "We expected to come off badly in the tables this year because our maths results were so low."
He was appointed two years ago to make "radical changes" and added: "I said at the time it was going to be a five-year programme."
Ofsted had acknowledged children arrived at the school with "very low levels of communication ability".
The school serves an ex-mining community that suffers from high unemployment rates and where heroin abuse is rife, said Mr Ball.
"I think most of the children in the school are affected by it in some way," he said.