The prince and Middleton, both 23, were initially planning to set up home in London, but Charles invited them both to stay together at his royal residence in Clarence House, London instead, reports British newspaper the Daily Express.
But William, second in line to the throne, will one day be head of the Church of England and religious figureheads are likely to condemn the move as "living in sin".
A source tells British newspaper The Daily Express, "Kate has already got some of her clothes and possessions in wardrobes inside William's apartment.
"She has stayed with William at Highgrove before so she's happy and comfortable in such surroundings. Prince Charles and Camilla both adore Kate and they can see how happy she makes him.
"He knows there will be people who kick up a stink put Charles is determined that William and Kate are happy together. There is a strong feeling in the Royal Family that Kate is perfect for William."