While neither actor has commented on the controversy, the producers of the Netflix series are now speaking out and taking responsibility.
The furore erupted last week when producers admitted that Smith, who plays the queen's husband Prince Philip, negotiated a better deal than Foy because of his perceived higher profile.
The revelation that Claire Foy was paid less than her co-star Matt Smith in The Crown, even though she plays the Queen, was met with outrage last week - and now the production company behind the Netflix series has apologised for the actors' pay inequality.
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". "Claire and Matt are incredibly gifted actors who, along with the wider cast on 'The Crown' have worked tirelessly to bring our characters to life with compassion and integrity", Left Bank said.
"As the producers of The Crown, we at Left Bank Pictures are responsible for budgets and salaries; the actors are not aware of who gets what, and can not be held personally responsible for the pay of their colleagues", the company added.
Left Bank Pictures said it is "absolutely united with the fight for fair pay, free of gender bias, and for a rebalancing of the industry's treatment of women". "As company policy we are engaged in conversations with ERA 50:50 and going forward are keen to talk to Times Up UK; organisations which are working to ensure all women have a voice".
They did not reveal either salary - Foy's was put at $40,000 an episode by Variety previous year - but told a panel event in Jerusalem that Smith's 2010-2013 starring role on the BBC's "Doctor Who" had been the decisive factor.
Claire Foy and Matt Smith in the first season of The Crown.
Foy played Queen Elizabeth in The Crown's first two seasons, and will be replaced by Olivia Coleman in Season 3 as the show's timeline progresses.
Suzanne Mackie, one of the show's producers, said the discrepancy was being resolved for the third season but that will not benefit Foy.