Four victims -- ranging from the ages of 18 to 35 -- were last week linked to the unusual weather phenomenon, where a thunderstorm coincided with a high pollen count and sent more than 8,500 patients to hospital emergency departments.
The rare event in Australia's southern state of Victoria triggered respiratory problems for asthma and hay fever sufferers.
"There have now been six deaths that may have occurred as a result of conditions relating to the thunderstorm asthma events on Monday," Victoria's health department spokesman said in a statement.
A further 12 people were being treated for respiratory and other health problems, he added.
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No further details were released about the two latest victims.
Victorian Health Minister Jill Hennessy said on Thursday that the demand for ambulances was so acute at one point that "it was like having 150 bombs going off right across a particular part of metropolitan Melbourne".
The government has launched a review into how emergency and health services can better respond and manage such rare events.