School leaders have warned that a growing number of missing or wrongly allocated marks on Key Stage Two Sats papers is “shaking confidence” in the assessment.

The NAHT school leaders’ union, which represents the majority of primary schools in England, said it is concerned about the management of end-of-primary Sats after schools have this year complained of missing marks or incorrectly allocated results for some pupils.

The union said it has voiced its fears with the Department for Education and the Standards and Testing Agency – but said it has been given no clear answers about the scale of the problem.

NAHT general secretary Paul Whiteman said: “As things stand, the Government is unable to tell us just how many children have been given incorrect marks for their Sats this year and how many papers have gone missing.

“This is a deeply worrying position to be in. If the Government is unable to identify the scale of the problem, how can leaders have confidence that they will be able to fix it?”

NAHT has been contacted by schools that have not only been told that some completed Sats papers have gone missing, meaning that their pupils will not be given a result, but also by schools where marks have been assigned to the wrong pupils.

Mr Whiteman said: “It is unacceptable for the answer to the Government’s failed Sats delivery to be for children not to be given any marks at all for their work. Parents will understandably be outraged by that.

“And for schools to then find, on closer investigation, that some of the marks they have been given are incorrect hints at complete chaos. It should not be up to schools to have to spend hours double-checking everything they’ve been told.

“The delivery of these tests has been beset with problems from start to finish. We need an immediate investigation into what has gone wrong and the Government must take urgent action to fix it.”

A poll by Teacher Tapp last week suggested that 20% of primary teachers had KS2 Sats papers with missing marks.

Mr Whiteman added: “If schools are obliged to spend the time implementing these tests, the least parents and children should be able to expect is a system that operates well.

“For a Government that prides itself on efficient delivery, this is the latest in a long line of failures and mismanagements when it comes to exams and assessments and it simply isn’t good enough.

“School staff all play their part, take it seriously and do exactly what is expected – and the penalties for mistakes are severe. We should be able to expect the same standards from Government.

“This needs to be put right urgently and the Government needs to listen to school leaders on what has gone wrong so that it does not happen again.”