The ship was set to arrive in Bali on Monday, and then sail to Perth as part of a 17-day voyage.
A spokesperson for Cunard said that, unfortunately, due to the ongoing rise in community transmission across Australia and that being reflected on various cruise lines, they were unable to visit Indonesia at this time.
"That has followed ongoing conversations with the respective authorities in Bali, and we understand and respect the current circumstances we're operating in.
"In light of this, we will sail into Fremantle in the coming days as planned."
The ship has max capacity 2500 passengers (2081 lower berths). The WA government said it had received information that 10 to 15% of the people on board were COVID-positive.
WA Health confirmed the cruise ship is expected to arrive in Fremantle (Perth) on Wednesday, November 30. Over the past 10 days Queen Elizabeth has also sailed to Airlie Beach, Cairns, and Port Douglas (Queensland).
According to a spokesperson for Cunard Line, 95% of passengers above the age of 12 were required to be vaccinated, with the remaining 5% of slots for people with medical exemptions. Free rapid antigen tests were available to all passengers and it was protocol for positive cases to enter isolation for 5 days.
Passengers could only come out of their 5-day isolation period after returning a negative rapid antigen test, the cruise operator revealed.
Meanwhile, WA recorded a total of 10,520 new COVID cases in the latest 7-day reporting period (16% increase on the previous week).
The outbreak on Queen Elizabeth comes after another ship, Majestic Princess, docked in Sydney NSW with 800 COVID-positive passengers onboard earlier this month.
For more Queen Elizabeth incidents and accidents see the ship's CruiseMinus page.