He reportedly took over direction from Alex Kurtzman, who was making just his second feature film, "often dictating the major action sequences and micro-managing the production".
He also reportedly hired new scriptwriters to beef up his role, adding a plot twist and turning the film from "a scary summer popcorn movie into a standard-issue Tom Cruise vehicle". He was also present in the movie's editing suite.
A statement from Universal denied Cruise's influence affected the movie.
"Tom approaches every project with a level of commitment and dedication that is unmatched by most working in our business today.
"He has been a true partner and creative collaborator, and his goal with any project he works on is to provide audiences with a truly cinematic moviegoing experience."
Cruise is currently in New Zealand filming Mission: Impossible 6.