The actor, who played 007's gadget-master Q in 2012 hit Skyfall, wed Australian composer Mark Bradshaw at a service in Sydney last August.
They have been a couple since meeting on the set of 2009 movie Bright Star, when Whishaw was playing poet John Keats and Bradshaw was composing the film's score.
A spokesman for the actor tells Britain's Mail on Sunday newspaper, "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."