Holmes, who plays an investigative reporter, and Eckhart, who plays a tobacco lobbyist, had filmed a racy romp for the film.
The sexy scene was still included in the film when it debuted at last year's Toronto Film Festival.
But it has now vanished from the version shown at the Sundance Film Festival - causing some to wonder if Holmes' fiancé, Tom Cruise, used his influence to remove the footage.
A spokeswoman for Fox Searchlight, who produced the film, said:
"It has never been altered.
"It will be released with that scene. We don't know what happened, but we're looking into it."
When director Jason Reitman was asked about the missing sequence during a press conference, he joked that it had been lost in a "technical glitch" during a reel change.
Responding to the same question at another screening, Reitman said:
"If you want to see a sex scene with Katie Holmes, rent 'The Gift'" - a reference to the 2000 film in which the former 'Dawson's Creek' beauty appears topless.
Tom Cruise wants Katie all to himself - movie or no movie.
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