The Very Reverend Kelvin Holdsworth made the comments in a blog post that he shared on Twitter encouraging people to pray "for the Lord to bless Prince George with a love, when he grows up, of a fine young gentleman".
Holdsworth is from the Scottish Episcopal Church, which voted in favour of gay marriage earlier this year, unlike in the Church of England where same-sex marriages are not allowed.
The blog post, which he published over a year ago but resurfaced after Prince Harry and Meghan Markle's engagement, saw him comment on LGBT marriage in the Church of England: "A royal wedding might sort things out remarkably easily though we might have to wait 25 years for that to happen."
Holdsworth has since published a clarification, expressing regret that it had led to a focus on Prince George and saying that it had not been his intention to cause hurt.
"The post was entirely about the church and its policies around LGBT inclusion," he wrote. "I would urge others, those who agree with me strongly and those who disagree with me strongly to turn our attentions to the actual matter at hand."
His comments drew criticism and were labelled "unkind" and "destructive" by one member of the Episcopal Church.
"To use prayer as a mechanism for wishing this on Prince George is an unkind and destructive thing to do," Gavin Ashenden, a former chaplain to the Queen and a Christian Episcopal Church missionary bishop told the BBC.