The actor, who stars as the titular daredevil archaeologist in the franchise, sustained the injury in a choreographed fight scene and will be now out of action while he recuperates.
It is a fresh blow for the movie - which sees James Mangold taking on directing duties from long-time helmer Steven Spielberg - after shooting was previously pushed back amid the coronavirus pandemic.
An insider told The Sun newspaper's Bizarre column, "It is Harrison's last outing as Indiana and everyone thought it would be plain sailing."
"After the initial delays everyone was raring to go. But now Harrison is injured and it is worse than first thought."
"The film's bosses have come together to work out the scheduling and it's chaos. The earliest they think they can restart the production is September."
"It was not what anyone was expecting so to have to change everything is a huge blow. Everyone was concerned for Harrison and they are glad he is on the mend."
Harrison is known for doing his own stunts on set and Spielberg confessed that he was an "idiot" for letting the star take on risky scenes such as the boulder run in "Raiders of the Lost Ark".
The legendary filmmaker said, "A double would have cheated his head down, so Harrison volunteered to do it himself."
"There were five shots of the rock from five different angles - each one done twice - so Harrison had to race the rock ten times.
"He won ten times - and beat the odds. He was lucky - and I was an idiot for letting him try it."