The vehicle runs over about half a dozen of them, with the driver counting along and laughing.
About 20 seconds later, the video shows the auto approaching a mob of emus which are running away from the vehicle.
Authorities have appealed for information, describing it as apparent evidence of "horrific cruelty".
In 2013, another Australian man faced similar animal-cruelty charges after posting a video of himself riding an emu to work like a horse.
Before the video ends the camera turns around to show a young man with a moustache, wearing a cap and sunglasses, who continues to laugh and scream "yes" at the camera before the video ends.
The man can be heard laughing and cheering as he ploughed full speed into the terrified birds, counting as he mowed them down one-by-one.More news: FedEx Cup to offer $15 million to winner next year
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The Cowangie man will be charged on summons with animal cruelty, animal torment, destruction of protected wildlife and traffic offences.
"This is great - I've got that one too, and that one", he says.
"The community is understandably outraged and angry about this vision - as are we", the group's acting chief inspector, Cheryl Doudle, said in a statement published by SBS News.
"Please do not "name and shame" alleged suspects on social media".
The accused will face a Victorian court in November.
The animal welfare organisation on Thursday pleaded for help to identify him and is now working closely with police.