Hooper left the field in the first half of Exeter's clash with Bristol over the weekend after picking up "a bang" on the same shoulder he injured while playing for Australia against Ireland in July, when he suffered a hairline fracture of the scapula.
The 25-year-old was sidelined for seven weeks and missed four Tests, against France, Italy and Japan in Osaka and Townsville, before returning in late August against Argentina in Salvador de Jujuy and then South Africa in Perth. He underwent scans on Monday, leaving Wallabies coach Les Kiss waiting on the results ahead of the tour opener in London.
Hooper and Taniela Tupou missed the Bledisloe series in October after returning to their clubs in England and France respectively, but both were named last week to rejoin the Wallabies for November as "Giteau Law" selections, along with Hunter Paisami of Japan.
"He got a bang on his shoulder, which he hurt before, hopefully it is not a bad injury," Exeter director of rugby Rob Baxter said after the match. "He will probably have to have a scan on it. Hopefully he has just aggravated it, but we won't know properly for a little while. It is the shoulder he hurt playing for Australia against Ireland."
The Wallabies are due to begin training in London next week ahead of the first-up clash with England at Twickenham. Another fracture would likely rule Hooper out of the four-Test tour.
Kiss and the coaching staff have this week formulated contingency plans, with six-Test back-rower Nick Champion de Crespigny on stand-by. With Charlie Cale also out injured, the Force forward replaced Hooper on the bench for the opening Bledisloe Cup clash in Auckland after the Exeter star returned to his club.
The Wallabies' back-row stocks are shallow owing to injuries to Cale, Pete Samu and Langi Gleeson. Other options include Brumbies lock-back-rower Toby Macpherson, who is on tour with Australia A in the United States, Reds back-rower Joe Brial, and two-Test back-rower Josh Kemeny, who has been in dominant form for Northhampton.