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Emergency crews were called to a property on Richardson St, in St Kilda, about 2.30am.
Authorities said a mother and three children escaped without injuries.
However, a Fire and Emergency New Zealand spokesperson said the house was extensively damaged and had left the family with nothing but the pyjamas they were wearing when the fire broke out.
It is understood the family is getting help from Victim Support.
Fire authorities said the blaze is not being treated as suspicious, but the cause is still yet to be confirmed.
There was clear damage to the outside of the house, including broken windows.