On Tuesday, the Minister for Women and Equalities, Maria Miller, announced that the Bill would include a "quadruple lock" of measures that would "protect religious freedom".
These would specify that it would be illegal for any Church of England minister to conduct a same-sex marriage.
But at a meeting with Parliamentarians on Thursday, the Bishop of Leicester, the Rt Revd Tim Stevens, said that this level of protection had not been mentioned in meetings with the Government.
He regretted that no prior consulation had been sought.
Mrs Miller said that the legal locks, "which will be on the face of any primary legislation, are:
• no religious organisation, or individual minister, could be compelled to marry same-sex couples (or to permit this to happen on their premises);
• it will be unlawful for religious organisations, or their ministers, to marry same-sex couples unless the organisation's governing body has expressly opted in to do so (and that would mean the religious organisation itself opting in, the presiding minister having consented and the premises in which the marriage is to be conducted having been registered);
• the Equality Act 2010 would be amended to ensure that no discrimination claim could be brought against religious organisations or individual minister for refusing to marry a same-sex couple (or allowing their premises to be used for this purpose); and
• the Bill will explicitly state that it would be illegal for the Church of England and the Church in Wales to marry same-sex couples, or to opt in to do so. Canon law - which bans the marriage of same-sex couples - will continue to apply. That means that it would require a change in both primary and canon law before the Church of England and Church in Wales would be able to opt in to conduct same-sex marriages."
The Bill will allow same-sex couples to get married in civil ceremonies, and for religious organisations - apart from the Church of England and the Church in Wales - to "opt in" and conduct marriage ceremonies for same-sex couples.
Mrs Miller said: "I feel strongly that, if a couple wish to show their love and commitment to each other, the state should not stand in their way. These changes will strengthen marriage in our society. . .
"I am absolutely clear that no religious organisation will ever be forced to conduct marriages for same-sex couples, and I would not bring in a Bill which allowed that. European law already puts religious freedom beyond doubt, and we will go even further by bringing in an additional 'quadruple legal lock'."
In the House of Commons on Tuesday, Mrs Miller said: "Because the Church of England and [Church in] Wales have explicitly stated that they do not wish to conduct same-sex marriage, the legislation will explicitly state that it will 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."
Should those Churches choose to opt in, ministers would still be able to refuse to officiate.