Russell Hobby, general secretary of the National Association of Head Teachers (NAHT), said the results were "excellent news".
"It shows the hard work that's going on in the system and has been going on for some years."
He said the majority of primaries will not be academies, which shows that schools can improve "no matter what their status".
This year's top-ranking school, for the second year running, was Newton Farm Nursery, Infant and Junior in Harrow.
It gained the highest average points score at 34.1.
- 1. Newton Farm Nursery, Infant and Junior School, Harrow: 34.1
- 2. Grinling Gibbons Primary School, London: 33.9
- 3. Bishop Gilpin CofE Primary School, London: 33.1
Pupils sitting the National Curriculum tests are given a set number of points for the level they achieve.
Level 2 or below is worth 15 points, Level 3 is worth 21 points, Level 4 is worth 27 points, Level 5 is worth 33 points, Level 6 is worth 39 points.
Each pupil's points for English and maths are added up and divided by the number of tests taken to give a school's average points score.
Schools with less than 30 pupils are not included.
A Department of Education spokesman said that the aim of their floor target was to boost standards and "end years of chronic under-performance."
Today's figures demonstrate that schools have responded to the challenge.
The floor standards we introduced were tougher and have improved performance.
Heads, teachers and pupils deserve credit for meeting the challenge head on.
The latest league tables show how more than 15,000 primary schools performed in national curriculum tests - known as SATs - in English (reading and writing) and maths.
Under the Government's current target, schools are considered failing if fewer than 60% of 11-year-olds reach the expected standard - Level 4 - in English and maths SATs tests, and fewer youngsters make two levels of progress in these subjects than the national average.
The national average for English progress this year is 92%, and for maths it is 90%.
Schools that fail to reach this threshold are at risk of being closed and turned into academies.
The latest figures show that of the 521 schools which are below the bar, 45 have already closed, with 37 becoming academies.
The number of primary schools failing to give pupils a good grounding in the three Rs has halved in the space of a year, official figures suggest.
In total, 521 schools in England are below the Government's floor target for primaries, according to an analysis of data used to create new primary school league tables.
Last year, 1,310 schools were below the threshold.
The results show that schools have "responded to the challenge" that was given to them, the Department for Education (DfE) said.