The Church of England and the Church in Wales have expressed their "complete shock" at the government's plan to ban them from offering same-sex marriages, claiming they were not consulted over the proposed legislation, which would make them the only religious organisations to be legally barred from conducting the ceremonies.

On Tuesday the culture secretary and equalities minister, Maria Miller, offered a comprehensive guarantee that neither church would have to marry same-sex couples. Although the move was intended to reassure Tory MPs who are threatening a rebellion over the proposals, it was greeted with dismay by senior figures in both churches, who said they knew nothing of the legal plans until Miller made her statement to the Commons. The Church in Wales said that it would push to have the proposals amended.

The Right Rev Tim Stevens, bishop of Leicester and the Church of England's lead spokesman in the Lords, told a closed meeting of bishops, Lords and MPs that the government had not consulted the church on the proposal, adding that the church had never sought the government's so-called "quadruple lock" on gay marriage. He also expressed his regret at the government's lack of consultation.

A Church of England spokesman confirmed that the church had not been consulted over the government's plans, saying: "Bishop Tim is correct that the first mention of a 'quadruple lock' came when the secretary of state announced it in the Commons. We had not been privately informed of this prior to the announcement."

Miller had been due to meet the Church of England representatives last Thursday but she cancelled the meeting at the last moment.

The churches' claims pile further pressure on Miller, who came under fire in the Commons over the plans. It was announced that she is to face an investigation into her expenses by the parliamentary commissioner for standards after the Daily Telegraph alleged that she had breached rules over her second home.

Officials from the Department for Culture, Media and Sport (DCMS) are understood to have filled in for the culture secretary last week, and she is thought to have met representatives of the Church of England after the statement on Tuesday.

Although the Church of England's position on same-sex marriage is clear – its submission to the government's consultation in June this year stressed that "the canons of the Church of England define marriage, in accordance with Christ's teaching and the doctrine of the Church, as being between a man and a woman" – it is privately understood that there is astonishment within the church that it was not told about the final proposals.

A spokeswoman for Dr Barry Morgan, the archbishop of Wales, confirmed that the Church in Wales had not been consulted over the "quadruple lock" either, saying it had come "completely out of the blue" and had left the church "completely shocked". The spokeswoman said: "We feel it's a step too far and we weren't consulted and we're now looking into what we can do. We will be pushing to have it amended, I would imagine."

The spokeswoman said the church had submitted its views on the sanctity of marriage as part of the consultation, it had not anticipated that the government would act as it had.

"At that time, we thought that the government were saying that this law would be one that all churches would be able to opt into, so we were keen at that time to have sufficient legal safeguards around us to ensure that none of our clergy – or the church – would be prosecuted under equal opportunities [legislation]," she said. "But we had no idea that we would be completely exempt. There was no indication at all that, as a church, we would be completely exempt and it makes us look like we're exclusive and we're different to the other churches."

Under the government's plans, four separate elements would ensure that no religious groups would be forced to act against their beliefs: the framework would guarantee that no religious minister would be compelled to marry same-sex-couples; would allow religious organisations wishing to do so to opt in to conducting marriages; would amend the Equality Act 2010 so that no discrimination claims could be brought against religious groups or individual ministers for refusing to marry a same-sex couple, and would ensure that the canon law of the Churches of England and Wales would remain unaffected.

According to the last guarantee, if either church wished to conduct a same-sex marriage, changes would be needed to both canon law and primary legislation.

In her statement to MPs, Miller said: "Because the Church of England and Wales have explicitly stated that they do not wish to conduct same-sex marriages, the legislation will explicitly state that it would be illegal for the Churches of England and Wales to marry same-sex couples.

"This provision recognises and protects the unique and established nature of these churches. The church's canon law will also continue to ban the marriage of same-sex couples. Therefore, even if these institutions wanted to conduct same-sex marriage, it would require a change to primary legislation at a later date and a change to canon law. Additional protection that cannot be breached."

A spokeswoman for the DCMS insisted that relevant parties had been duly consulted, adding that the government had acted according to the church's wishes.

"As part of our consultation process, and as we finalised our proposals, government officials met with a number of stakeholders, including the CoE," she said. "Clearly, it would have been inappropriate to discuss the fine detail of our proposals prior to them being announced in parliament. But the church made clear to us its wish to see legal provisions which would ensure that their position on not conducting same-sex marriages would continue."

The Labour MP Ben Bradshaw, who was at the Lords meeting, said Stevens' revelation that the church had not been informed had drawn "audible gasps" from members of all parties.

"It's absolutely extraordinary," he said. "The government gave the clear impression that this had been done at the request of the Church of England … but the bishop of Leicester said: 'We didn't ask for it' … and was very upset about it because it gave the impression that the Church of England were unfriendly towards gays."

Asked why the government had chosen to propose the "quadruple-lock" guarantee, Bradshaw said: "The only explanation I can think of was that they thought it would help placate some of their homophobic backbenchers. But it seems to have backfired massively because the rightwing homophobes were out in force anyway and the Church of England now appears to be extremely upset that not only was it not asked, but it's added to [the] general misery over women bishops and now this. It makes the Church of England look much more reactionary and unreasonable than it actually is," he said.