Video seen on the private Nova television channel showed the bus, and then other vehicles, being hit by an all-wheel-drive vehicle that appeared to have braking problems.
"It happened in a closed area that was rented out to the filmmakers for the weekend," said Prague police spokeswoman Eva Brozova.
Jirina Ernestova, spokeswoman for the emergency services, said the injured were treated in hospitals in the Czech capital.
"According to my information, there were only slight injuries," said David Minowski from the local production house Stilling Films.
Directed by Stephen Sommers, "G.I.Joe" -- starring Channing Tatum, Dennis Quaid and Sienna Miller -- is a live-action feature based on the eponymous action figure that is due out in August 2009.
In April 2002, a stuntman from the United States was killed in Prague during the filming of the Rob Cohen action film "Triple X".