The 3,000 or so residents of the blocks are being told not to leave their homes for any reason for at least five days.
At least 23 cases of infection were found on two estates in recent days.
The state of Victoria recorded 108 new cases on Saturday, its second-biggest daily increase. Australia as a whole has seen 104 coronavirus deaths.
There have been at least 8,362 infections nationwide.
Victoria State Premier Daniel Andrews said the latest figures there were a very real concern to everybody.
How different is the response in Melbourne?
The city is putting "stage three" restrictions on 12 suburbs. People there will only be able to leave the house for four reasons: work or education, exercise, medical care or care-giving, and shopping for supplies.
But the nine tower blocks in Flemington and North Melbourne face a "hard lockdown".
According to Victoria's Minister for Housing, Richard Wynn, some of the state's most vulnerable people live in the nine towers, and mental health and drug and alcohol support will be offered.