On The Graham Norton Show, Beckinsale said, "I think he was baffled by me because my boobs weren't bigger than me head and I wasn't blond.
"I'd just had my daughter and had lost weight... But I was told that if I got the part, I'd have to work out and I just didn't understand why a 1940s nurse would do that."
Bay took to his website to clear the air in the wake of Beckinsale's comments, which were widely reported.
The director said he "spoke to Kate today and she felt she told a funny story" on the late-night show.
"So I guess I was the 'bad guy' 16 years ago for suggesting a trainer because she just had had her new beautiful baby girl-and she was about to enter into an intensive action movie," he wrote before noting, "95 per cent of leads in movies have trainers and drink green juice!"