A primary school praised by ministers as a model academy “over-aided” pupils in this year’s national tests, a government investigation has concluded.

Year 6 pupils at Harris Academy Philip Lane in Tottenham, north London, were given too much help in their English reading and maths reasoning Sats, according to the Standards and Testing Agency (STA).

As a result, pupils’ scores in those papers have been expunged and they will receive scores only for their spelling, punctuation and grammar tests.

In a letter sent to parents on Monday, the academy’s chair of governors, Susan Head, described the investigation findings as “deeply regrettable and disappointing”.

She said the findings were being taken “extremely seriously” and responsibility lay with the academy rather than pupils. She said the school was “determined to get to the bottom of what has happened”.

The school’s principal, Emma Penzer, wrote to parents before the summer holiday to tell them the Sats results would be delayed because of the investigation.

The Harris Federation is often hailed as one of the most successful academy trusts in England. But Simon O’Hara, of the Anti Academies Alliance, which published the letter on Twitter, said: “What confidence can other parents whose children attend Harris academies have in what is going on in their schools? Academisation is becoming increasingly mired in cronyism and corruption. We believe that all schools should be returned to local democratic control.”

The investigation findings have infuriated campaigners who opposed the forced academisation of the school in Haringey, one of London’s most deprived boroughs, six years ago. The then education secretary, Michael Gove, ordered the former Downhills school’s takeover by the Harris Federation despite the opposition of 94% of parents.

The move came after an Ofsted investigation declared the school to be failing. Academies are accountable to central government rather than a local authority.

The ’lunatic’ Gove cut his teeth in the fight to hand over Downhills to Harris Federation. In the face of overwhelming opposition he forced academisation. He promised a better education. This is what happened: @cyclingkev @schooltruth @DavidLammy pic.twitter.com/13W8dhQVFH — Anti Academies (@antiacademies) August 8, 2018

Fiona Millar, a school governor and campaigner on education issues, said: “A lot of us have been concerned that certain academy chains have been held up as an example of what everyone else should be as good as. I’m a governor of two London schools and I’ve scrutinised their data and wondered how they get these results with similar cohorts of pupils. Increasingly we see they do it by this unethical behaviour. It’s really hard on the schools that are playing by the rules because they can never hope to compete.”

Madeleine Holt, an education campaigner and co-founder of Rescue Our Schools, said: “If you create a high-stakes system where schools are punitively judged on Sats scores, gaming and cheating is one of the many damaging consequences. There are better ways to judge schools and students – for example in New Zealand, where they have got rid of their equivalent of Sats and are developing broader and fairer ways of evaluating education. This can’t happen soon enough in England’s primaries.”

The Harris Federation said it was “shocked and dismayed to hear of the over-aiding” and would conduct an internal investigation in light of the STA’s finding. “This will begin in the autumn term and we will not hesitate to take the very toughest action wherever this is appropriate,” a spokeswoman said.

She said the academy had apologised to families whose children had not received their maths or English reading Sats results. “Pupils have been given accurate teacher assessments and these have been provided to the secondary schools they are moving on to, along with their grammar, punctuation and spelling results. This will ensure their transition to secondary school is not affected.”

A Department for Education spokesman said: “Teachers and parents must have confidence in the integrity of the assessment system, which is why we take allegations such as this very seriously. Following an investigation by the Standards and Testing Agency, several key stage 2 papers were annulled. This will not, however, adversely affect any of the pupils as the school can provide teaching assessment data to show the pupils’ progress in these subjects.”