Henry Cavill is understood to have left Simon West's Stratton with just a week to go until filming starts.
It's left the director scrambling to find a replacement lead before cameras start rolling.
The film is hoped to be the first in a franchise based on books by ex-serviceman Duncan Falconer; the first one is based around John Stratton - a special forces operative who works with MI6 to shut down a global terrorist cell.
Empire reports (via Screen Daily) the Man of Steel's exit is down to not being able to make changes he had suggested to the shooting script.
That seems to be backed up by comments from Guy Collins, co-founder of the film's financiers GFM Films: "[Cavill] told us he has decided not to shoot this script at this time."
"He had a different vision of what the film should be to us and the production team and wanted to delay production until September and shoot a different story and script."
Cavill and his brother's production house Promethean Productions had set up the project - so a delay whilst further agreements are made seems inevitable.
It follows news Cavill's The Man from UNCLE directed by Guy Ritchie will premiere at Film4's Summer Screen in August.