Children should be able to try out “the many cloaks of identity” without being labelled or bullied, the Church of England has said in new advice issued to its 5,000 schools.

The Church said youngsters should be free to “explore the possibilities of who they might be” – including gender identity - and says that Christian teaching should not be used to make children feel ashamed of who they are.

Nursery and primary school is a time of intense “creative exploration”, the fresh guidelines say, and children should be able to choose the tutu, tiara and heels, as well as or instead of the helmet, tool belt and superhero cloak “without expectation or comment”.

Guidance for Church of England schools on homophobic bullying was first published three years ago, and has now being updated to cover "transphobic and biphobic bullying" – which means bullying people who consider themselves to be either transgender or gender fluid.

The guidelines warn that schools must take action to stamp out bullying based on perceived or actual sexual orientation or gender identity, because of the psychological damage it can cause.

The guidelines say that schools which “promote dignity for all” enable pupils to “accept difference of all varieties and be supported to accept their own gender identity or sexual orientation and that of others.”

The advice goes on to say: “In the early years context and throughout primary school, play should be a hallmark of creative exploration.

”Pupils need to be able to play with the many cloaks of identity (sometimes quite literally with the dressing up box). Children should be at liberty to explore the possibilities of who they might be without judgement or derision.

“For example, a child may choose the tutu, princess's tiara and heels and/or the fireman's helmet, tool belt and superhero cloak, without expectation or comment.”

It adds: “Children should be afforded freedom from the expectation of permanence. They are in a 'trying on' stage of life, and not yet adult and so no labels need to be fixed.

”This should inform the language teachers use when they comment, praise or give instructions.

“It may be best to avoid labels and assumptions which deem children's behaviour irregular, abnormal or problematic just because it does not conform to gender stereotypes or today's play preferences.”

In a foreword to the advice, the Archbishop of Canterbury says: “All bullying, including homophobic, biphobic and transphobic bullying causes profound damage, leading to higher levels of mental health disorders,self-harm, depression and suicide.

“Central to Christian theology is the truth that every single one of us is made in the image of God. Every one of us is loved unconditionally by God.

“We must avoid, at all costs, diminishing the dignity of any individual to a stereotype or a problem.”

The Most Rev Justin Welby adds: “This guidance helps schools to offer the Christian message of love, joy and the celebration of our humanity without exception or exclusion.”

The guidance acknowledges a wide range of views among Christians and people of all beliefs about same-sex marriage, sexual orientation and gender identity.

The new guidelines are likely to reignite the debate around the idea of children being allowed to “self identify”, with critics asking whether there is a sudden “trend” towards gender fluidity and gender neutral.

Campaign groups including Christian Concern have raised concerns that any dissenting voices in the debate around gender identity are being silenced or labelled as bigoted.

A Christian Maths teacher from Oxfordshire is due to appear before a disciplinary hearing to answer allegations that he referred to a pupil born female as a “girl”.

Joshua Sutcliffe claims not to have been given any instructions on how to refer to the pupil, and said he did not mean to cause any offence.

According to Christian Concern: "Since the pupil started at the school, Joshua has tried to balance his sincerely held Christian belief that biological sex is God-given and defined at birth, with the need to treat sensitively the pupil. He avoided the use of gender-specific pronouns, and instead referred to the pupil by the pupil’s chosen name. Joshua admits saying “Well done girls” when he addressed a group of students including the pupil in question. The pupil became irate at this and Joshua sought to diffuse the situation and apologised”

Responding to the proceeding against him, Mr Sutcliffe said: “I have been shocked and saddened by the actions of the school, which, in my opinion, reflect an increasing trend of seeing Christians, people like me, being marginalised in the public square, and our beliefs punished and silenced.

“While the suggestion that gender is fluid conflicts sharply with my Christian beliefs, I recognise my responsibility as a teacher and Christian to treat each of my pupils with respect and dignity.”

“I have balanced these factors by calling the pupil by the chosen name and although I did not intentionally refer to the pupil as a ‘girl’, I do not believe it is unreasonable to call someone a girl if they were born a girl.

“The aggressive way in which transgender ideology is being imposed is undermining my freedom of belief and conscience, as well as the conscience of many people throughout our nation who believe that gender is assigned at birth.”

Lonely road: Why school is hell for transgender pupils Show all 2 1 /2 Lonely road: Why school is hell for transgender pupils Lonely road: Why school is hell for transgender pupils Many schools experience difficulties when faced with a pupil who does not fit neatly in to the 'boy' or 'girl' box © Alamy Lonely road: Why school is hell for transgender pupils Urgent reform: Stephen Whittle, a transgender professor, is pushing for greater protection of trans pupils in schools © Warren Smith

Andrea Williams, chief executive of the Christian Legal Centre which is supporting Mr Sutcliffe, said: “This case is one of a flood of cases we are encountering where teachers are finding themselves silenced or punished if they refuse to fall in line with the current transgender fad.

“We all know how much we change during our teenage years. It is vital that during those years we help our children to live in the biological sex they were born rather than encouraging them to change ‘gender’. If we encourage them to change gender it is not kind and compassionate; it is cruel.”

The case comes after genetics expert and Labour member of the Lords, Professor Lord Robert Winston, said that transgender people can end up "damaged”.

In an interview on BBC Radio 4's Today Programme, he said: “What I’ve been seeing in my fertility clinic is the long-term results of often very unhappy people who are now quite badly damaged.”

Figures published this year by the Gender Identity Development Service, based at the Tavistock Centre in north London, reveal the number of very young children aged between three and seven being referred to the clinic because of confusion about their gender had more than quadrupled from 20 in 2012-13 to 84 last year.