Kelvin Holdsworth tweeted that English people could "pray in the privacy of their hearts (or in public if they dare) for the Lord to bless Prince George with a love, when he grows up, of a fine young gentleman".
"A royal wedding might sort things out remarkably easily though we might have to wait 25 years for that to happen," said Holdsworth, who is from the Scottish Episcopal Church.
The Scottish Episcopal Church, a branch of the Anglican Church, voted in June to remove the reference in the wedding ritual to marriage being a union "between a man and a woman". It has since celebrated several same-sex marriages.
Anglican leaders in October disciplined the Scottish Episcopal Church in the same way as they did the US Episcopal Church in 2016 for approving gay marriage.
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Gavin Ashenden, a former chaplain to Queen Elizabeth II, condemned Holdsworth's remarks.
"If you're going to pray for Prince George, pray for him to be happy... and pray for him to discharge his duty as prince, to be married and have children," he told The Times.
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