The controversial check will be introduced in schools next month and will be taken by all children at the end of Year 1.
Ministers believe that systematic synthetic phonics is the method proven to improve reading standards for all children, including the weakest readers.
But critics of the test, which involves children reading aloud a mixture of real and made-up words, say that it does not give a true picture of children’s reading ability or comprehension.
Just 32 per cent of the Year 1 pupils in 300 schools who took a trial run of the test last summer passed it.
Speaking at the National Association of Head Teachers conference in Harrogate at the weekend, the union's general secretary Russell Hobby said that if the phonics screening check was not used as a proper assessment the union would join forces with other teaching unions such as the National Union of Teachers to stop the test.
Mr Hobby said, ‘We fear that the pass rate for the new phonics screening check will be set at an arbitrary high level in order to fuel headlines about children failing to learn to read.’
He added, ‘There is not yet a robust evidence base for any particular pass rate. We don’t see the need for this screening check – it is inferior to what most schools do already – but if it is to happen it should be used as a genuine diagnostic test, not a stick to beat schools with.
‘And if it is used to attack rather than assess, that will be the end of the screening check as far as the NAHT is concerned. And we will happily work with our colleagues in other unions like NUT to frustrate its further application.’
Mr Hobby’s speech also talked about concerns that schools are being forced to become academies.
He said the association had worked successfully with several schools resisting becoming academies, and that he believed that the vast majority of primary schools would retain their maintained status.
‘Not every school will become an academy or wants to do so. It must not be the only tool in the box. When ministers highlight the half of schools becoming academies, they mean secondaries. And they are in danger of forgetting about the 97 per cent of primaries that have not yet gone down this route,' he said.
‘I believe that the vast majority of 17,500 primary schools in this country will remain maintained schools. The fear of being "the last school left in the LA" is unfounded. I want schools to know that they have a very real choice, not to be overwhelmed by momentum, to be able to follow their education values.’