The Prince of Wales is said to have raised his fears of "unintended consequences" of the government rushing to change the laws of succession to the throne.
In a private meeting with Richard Heaton, permanent secretary of the Cabinet Office, Charles reportedly voiced concerns over what would happen if his grandchild, due next year, were to marry a Roman Catholic.
The succession to the crown bill, which will change the ancient laws governing the royal line of succession to ensure the Duke and Duchess of Cambridge's first child would succeed to the throne regardless of gender, has been published and is expected to be fast-tracked through parliament at the earliest opportunity.
The planned reforms, presented by the deputy prime minister, Nick Clegg, would also allow the couple's first-born to marry a Catholic – though not to be one, without having to renounce the right to succeed.
Sources told the Daily Mail Charles outlined to Heaton concerns that the move, which he is said to support in principle, could damage the relationship between church and state.
Echoing concerns raised previously by constitutional experts and theologians, Charles reportedly raised the issue of what would happen if his grandchild's future spouse were Catholic and insisted any children be raised as Catholics. This would either bar their child from the throne or compromise the monarch's role as supreme governor of the Church of England.
Canon law does not stipulate that children from a marriage between a non-Catholic and Catholic must be raised in the Catholic faith. But the Catholic must make a declaration "that I will sincerely undertake that I will do all that I can within the unity of our partnership to have all the children of our marriage baptised and brought up in the Catholic church".
The Mail reports that Charles was told during the meeting that any issue could be resolved by negotiations with the Vatican as and when the matter arose. It says Charles found this answer unsatisfactory and unconvincing.
He is also reportedly concerned about the lack of detailed consultation over the bill, which was announced on the day the Duchess of Cambridge made news of her pregnancy public. The paper said it was thought the Queen had not been informed of the decision to legislate until very soon before the bill was published, and her son and grandson appeared not to have been consulted at all, "which rankled with the Prince of Wales".
Charles is also said to have raised concerns over the effects of the proposed abolition of primogeniture, where a male sibling takes precedence over an older female, on other dukedoms and on the hereditary peerage in the UK.
Neither the Cabinet Office nor Charles's official office would comment on details of any meeting. A Clarence House spokesman said it was a matter for government.
