The 55-year-old actor, who is known for insisting on performing his own stunts, was jumping between two buildings with the assistance of a harness.
But he missed the edge of the second roof and banged into the side of the building with force during the incident on Sunday.
Footage obtained by TMZ.com showed Cruise then limping towards his team and collapsing onto his knees.
He was then lifted back over to the first building via his harness before limping out of view of the camera with help from his safety team.
The extent of his injuries are not known.
The actor and Scientologist is currently filming Mission: Impossible 6 , which is due for release in Summer 2018, in an unknown location is London.
Cruise was previously seen filming dangerous scenes for the movie in Paris, where he rode a motorbike into a car before flying through the air.
He was also photographed parachuting in Oxfordshire while filming at the beginning of this month.
The film's executive producer David Ellison previously said Cruise had been training for a year for the movie and was preparing to pull off his most "mind-blowing" stunt to date.
He said: "It is going to be, I believe, the most impressive and unbelievable thing that Tom Cruise has done in a movie, and he has been working on it since right after Rogue Nation came out. It’s going to be mind-blowing.”