Winging its way through Parliament, virtually unnoticed, is a piece of legislation that makes Section 28 pale into insignificance. It is actively discriminatory, in that it will allow gay people to be sacked purely because of their sexuality. What is more, it is apparently being backed by the Archbishop of Canterbury, Dr Rowan Williams, a noted liberal on the subject of gays.

How has this come to pass?

This is a question a lot of people in the Church of England — even, privately, some bishops — are asking. The law in question enacts the EU’s Equal Treatment Directive, which bans discrimination against gays. But the Church of England’s senior body, the Archbishops’ Council, has been granted an exemption which will allow churches and religious organisations to fire gay employees. This could even extend to teachers in Church of England schools or carers in old people’s homes run by the Church.

Friends of Dr Williams believe that he has been ambushed by reactionary elements in the Church’s bureaucracy. The Archbishops’ Council demanded the exemption in January, while he was on retreat before his enthronement. It was not acceded to by the Government until after the consultation on the directive was over, thus preventing any challenge. Because the regulations are secondary legislation, they cannot be voted down by MPs, except by throwing out the whole measure.

The only realistic way of stopping this exemption becoming law is for Dr Williams to ask the Government to withdraw it. But that would cause a huge row at the top of the Church and inflame passions that are already running perilously high over the issue of homosexuality.

Saturday may see the election of the first openly gay Anglican bishop, Gene Robinson, who looks set to become Bishop of New Hampshire. Meanwhile a Canadian diocese, New Westminster, last week authorised the blessing of same-sex unions, an action that has caused fury in Nigeria, one of the most active and conservative provinces of the Anglican Communion. No fewer than 17 million Nigerians — and rising — are practising Anglicans, compared with just a million in England. At home, petitions have been sent by evangelicals to the Bishop of Oxford protesting against the appointment to the Reading bishopric of the Rev Canon Jeffrey John, an avowed liberal on gay matters.

The irony is that homosexuality was the one issue that Dr Williams wanted to avoid having to address early in his primacy. Everyone knew that he had ordained a gay priest and that he saw nothing wrong with faithful gay relationships. But he did not want to impose these views on a Church that contained millions of worshippers who saw homosexuality as an abomination. Instead, he hoped that, by not rocking the boat, he would be able to conciliate both sides.

Instead, the conservative evangelicals have decided to rock the boat themselves. From the day of his appointment they have sent Dr Williams sacks of hate mail. They have threatened to withdraw funds from an already impoverished Church — and they are by far the richest part of that Church. Nigeria has declared itself out of communion with New Westminster, and the Primate of Nigeria called on Dr Williams yesterday to rescind the appointment of the new Bishop of Reading. It is evangelicals who are behind the exemption on the Equal Treatment Directive.

So far Dr Williams has barely resisted. He said he regretted the New Westminster action. The new Bishop of Reading has had to declare — presumably as a condition for taking the job — that he will not ordain gay priests, as stated in the notorious Issues in Human Sexuality. When the last Archbishop of Canterbury, George Carey, asked Dr Williams to support Issues as the price of becoming Bishop of Southwark, he refused to do so and was not appointed.

What is going on in the Church of England is medieval: like the Spanish Inquisition without the violence.Priests are being forced to affirm publicly views they do not hold privately. Dr Williams is being stretched on a modern-day rack, pulled in opposite directions by factions of the Church. The result is that he is leading a life as double as those of the many covertly gay priests in his care. What he believes privately is one thing; what he feels forced to declare publicly is another.

It has long been a scandal in an institution that preaches integrity that gay priests have been coerced into dishonesty. It is even more of a scandal that the leader of the Church can no longer be true to himself.

The trouble is that the two underlying principles of Dr Williams’ primacy are in fundamental opposition to each other. On the one hand, he is determined not to be the leader who presides over the schism of the Anglican Communion. Moves towards liberalism on homosexuality could threaten the unity of the Church. On the other hand, his big mission is to reconnect modern culture with Christianity. What hope has he of doing so when his institution is presenting itself as bigoted against gay people? The Church’s actions over the Equal Treatment Directive fly in the face of modernity.

Dr Williams is surrounded by a staff at Lambeth Palace appointed by his conservative predecessor, who urge caution at every step. They told him that he could not bring any staff with him from Wales, not even his trusted chaplain. Undemanding by nature, he has failed to insist on introducing allies into his office.

But he must soon start to assert himself a little, if only in his famously mild way. When a boat is still, it makes sense not to rock it; when it is already being rocked by someone else, an equal and opposite force must be exerted to stop it capsizing. Action on the Equal Treatment Directive would be a good start.

maryann.sieghart@thetimes.co.uk

Times Recommends

• Fragility always gets my sympathy vote
• Double it and you get the real jobless total
• Has al-Megrahi paid his council tax?