The production company apologized that Foy and Smith "have found themselves at the center of a media storm this week through no fault of their own."
The Netflix series traces Elizabeth's journey from princess to queen, beginning in the 1950s.
Trade publication Variety quoted producer Suzanne Mackie as confirming Foy was paid less than Matt Smith, who played Prince Philip in two seasons of the series. She made the reported comment at an industry event in Jerusalem.
She said this was because Smith was better-known after starring in sci-fi series "Doctor Who." Mackie said the gap would be closed with the forthcoming third series, saying "going forward, no one gets paid more than the queen."
Neither Foy nor Smith will appear in the third series, which will star Olivia Colman as the middle-aged monarch.
The gender pay gap has become a major issue in Hollywood after revelations that many female stars were paid less than their male counterparts.