Horrified Celia Mullen, 46, claims her son Luis and other children were encouraged to take part in the bizarre ritual by members of an evangelical church during a visit to his class.
She says the incident has left her son so disturbed that he now refuses to sleep on his own and scrawls pictures of the Devil.
Ms Mullen said the first she knew about the visit by the evangelical New Life Baptist Church was when her son came home from school upset.
She said he had asked her: 'Mum, why do I have to say sorry?' She says she replied: 'What do you mean? Did you do something wrong at school?'
'He then told me, "We had to eat a piece of paper with the word sorry on it." He started to cry.
'I comforted him and asked him why he thought he might have had to say sorry and he said he just didn't know.'
Celia sent her son to Ainderby Steeple primary near their home in Northallerton, North Yorks, because as a Church of England School she assumed he would get a traditional education.
But after he came home distressed she found a lesson plan given to pupils who had taken part in the church's 'Kidzone Roadshow'.
She said: 'It was called the Big Prayer Experience. On it was an explanation of the purpose of prayer.
'It went into the need for adoration of God and to ask God for help. It said, "We confess when we say sorry for something wrong. Today we are going to say Sorry to God. We will write sorry on a piece of paper and eat it". I was horrified.'
On the New Life Baptist Church's website it describes visits to local schools as 'an exciting programme of drama, music and games'
On another occasion Celia says Luis was sent home with an adult Bible having been told that it would 'make him good'.
At home Luis refused to sleep in his room and presented his mum with a picture he had drawn – of the Devil with horns, tail and a trident fork. Then he drew an angel.
'I couldn't understand why he drew a devil with horns and an evil face. Then he drew an angel,' said Celia, who works as a sales ledger clerk.
'Since all this happened Luis has not been able to sleep alone. It has left him disturbed.'
Celia says she complained to headteacher Fiona Sharp. She claims that when she confronted Miss Sharp over making pupils eat their 'apologies to God', written on rice paper, she was told: 'That is what we do.'
Celia has asked her local MP, Foreign Secretary William Hague, to investigate and has found Luis a place at another school. To her horror, she later discovered the church group make monthly day visits there too.
She said: 'I had no choice but to accept. There aren't any other schools around here they don't go into, but I have added that he must not attend these sessions.'
Another concerned parent who has asked not to be named has also switched his children's schools to avoid the prayer sessions.
He said: 'I have my religious beliefs, I have my faith, but this is indoctrination of young minds on an unprecedented scale.'
According to its website, the New Life Baptist church is 'a lively evangelical, charismatic church'.
Assistant pastor Steve Cowie confirmed the incident but added: 'We are sorry that anyone should be upset, we have no intention to upset, we do not intimidate, we do not force anyone to do anything.'
The school's board of governors is investigating the incident.
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