The City of Yarra mayor has lashed the government over the mapping, saying residents will bear the costs of inadequate infrastructure investment.
Home owners in another two council areas are being warned they are in danger of flooding from overflowing drains as new maps are released.
Hundreds of thousands of homes across Melbourne will be added to a new flood risk register that should guide suburban development and insurance premiums.
The government has released the first batch of maps revealing what a high-density future could look like for Melbourne residents.