The Queen did not believe gay marriage should have been allowed, a source told the Daily Mail.
The newspaper cites a "friend" as saying she favoured civil partnerships but because of her deep Christian faith, did not support same-sex marriage. This is because she believed the traditional Christian teaching that marriage should be between a man and a woman.
Same-sex marriage legislation was passed in England and Wales in 2013 and came into force in 2014. It was passed in Scotland in 2014. It is still not allowed in Northern Ireland.
The Queen reportedly told her friend she was frustrated but powerless to intervene.
The friend said: "I said to her, couldn't she do something about it, and she replied: 'I can't. I can only advise and warn.'"
The friend added: "It was the 'marriage' thing that she thought was wrong, because marriage ought to be sacrosanct between a man and a woman."
The article is the first in a series being published by the paper to mark Her Majesty's 90th birthday next month.
Buckingham Palace did not comment because it never comments on what are regarded as private matters.
The Queen is Supreme Governor of the Church of England, which strongly opposes gay marriage and secured protection from having to allow gay marriages to take place in its churches without a change in the law.
Last year Pink News reported a story recounted by comedian and actor Stephen Fry that the Queen thought gay marriage was actually a good thing.
Fry told the Jonathan Ross Show: "When the Queen signed the Royal Assent for the equal marriages act, allowing gay people to marry for the first time, she put it down and said 'Well, who'd have thought 62 years ago when I came to the throne, I'd be signing something like this? Isn't it wonderful?'"
Fry continued: "I am so proud to live in the country where [acceptance] seems to be the absolute majority view."
