The 32-year-old star ‘married’ his partner, Australian composer Mark Bradshaw, in Sydney last August.
The couple met on the set of Jane Campion’s 2009 film Bright Star, about John Keats’s heartbreaking love affair with neighbour Fanny Brawne before his untimely death from TB.
Whishaw played Keats in the film, while 30-year-old Mr Bradshaw composed the score.
The actor, widely hailed for his brilliance on stage and screen, thrilled audiences last year with his quirky high-tech take on MI6 boffin Q in the Bond film Skyfall.
His sexuality has been the subject of a lively internet debate in recent years. Speculation was sparked by an interview he gave to the gay magazine Out in March 2011 while playing a homosexual character in an off-Broadway play, The Pride.
When the interviewer asked whether it was important for young gay people to have positive role models, Whishaw replied: ‘I feel in my heart that it’s important, but I don’t quite know yet the way to go about that. Maybe that’s the transitional thing I feel I’m in the middle of at the moment.’
Last night Whishaw’s spokesman confirmed the civil partnership, saying: ‘Ben has never hidden his sexuality, but like many actors he prefers not to discuss his family or life outside of his work.
‘Due to speculation, I can confirm that Ben and Mark entered into a civil partnership in August 2012. They were proud to do so and are very happy.’
A friend of the couple, who live in Hackney, East London, said: ‘Everyone’s delighted for them. Mark’s a lovely guy, very talented and very close to Jane Campion. There hasn’t been a chance for a big celebration because of Ben’s schedule but I’m sure there will be one at some point.’