Campaigners including Peter Tatchell and the pressure group Republic have attacked the Queen's decision to send a supportive message to the Fellowship of Confessing Anglicans (FCA), a new traditionalist group within the Anglican Communion.
Peter Tatchell called her decision "a serious error of judgement which colludes with prejudice" and James Gray of Republic said it was “a catastrophic blunder”.
Anglican Mainstream, a pressure group supporting FCA said on its website today that it had written to the Queen after the Jerusalem conference, to express its concerns and "loyalty to her as the Supreme Governor of the Church of England."
They said that she had replied saying she understood "the commitment to the Anglican Church that prompted you and your brethren to write as you did".
The group said she then sent another message last week, expressing her encouragement for the launch of FCA today, and her "good wishes to all concerned for a successful and memorable event".
But human rights campaigner Peter Tatchell said: "The Queen has made a serious error of judgement. Her letter of support for the breakaway anti-gay faction of the Church of England is collusion with prejudice. She has insulted lesbian and gay people and breached royal protocol by embroiling herself in an issue of religious and political controversy."
His comments came after an earlier report in the Daily Telegraph which also said that the Queen had written twice to the Fellowship of Confessing Anglicans (FCA), offering her support, expressing her understanding and wishing them success.
"It is very alarming to see the Queen endorse a homophobic grouping within the Church of England. She is taking sides, against gay equality," added Mr Tatchell.
"Her Majesty is aligning herself with a Christian fundamentalist grouping that is founded almost entirely on its opposition to gay priests and gay human rights. Homophobic prejudice and discrimination is central to its religious ethos.
"Many leading members of FCA believe the civil and criminal law should discriminate against gay people. They do not believe that we are entitled to equal rights.
"That is why they opposed the gay law reforms of the last decade, including an equal age of consent, civil partnerships, protection against discrimination, the repeal of Section 28, fostering and adoption by same-sex couples, and access to fertility treatment for lesbian partners," said Mr Tatchell.
His criticism was echoed by Republic spokersperson James Gray who said: "This is a catastrophic blunder by the Queen. It gives the lie to the idea that she is politically impartial."
"This divisive move will cause huge offence and will force many to question the future of the monarchy."
"As the monarch she must remain silent on political issues. That's the deal with the monarchy: the Queen gets to wear the crown and live off the state, but she has to keep her opinions to herself."
"By publicly aligning herself with the FCA, the Queen has strayed not only into a religious debate but also a highly political one."
"At the heart of this split are the serious political questions of rights and equalities. It is absolutely unacceptable for the Queen to take sides."
"This row demonstrates the need for a new republican constitution. We need a fully accountable head of state whose views on such social issues are open to challenge."
Buckingham Palace said it would not comment on private correspondence. Royal sources said the Queen was not endorsing the FCA and pointed out that she corresponds with a great number of organisations.