The croc, measuring up to two metres (6.5 feet), "reacted defensively" when the swimmer "inadvertently" swum into it on Sunday near popular Lizard Island in Queensland state.
"The man suffered minor cuts and abrasions to his head and was treated for his non-life threatening injuries on the island," a department of environment spokesperson said.
"Wildlife officers are travelling to the area and will search the area for the crocodile responsible."
The waters surrounding Lizard Island are a known hotspot for crocs with signs in the area cautioning swimmers of the threat.
In a separate incident Sunday, a crocodile was found decapitated near Innisfail in Queensland, prompting authorities to warn it was illegal to kill the reptiles.
"Based on an initial inspection, the four metre animal appears to have been deceased for some time," the department spokesperson said.
Last month a fisherman was killed by a crocodile near Innisfail while a teenager was lucky to escape with only two broken bones when a croc latched onto his arm after he jumped into a river in the area.
Repeated attacks have lead to calls from some parts of the community for a cull of the animals, but the state government has so far resisted, saying it would have little effect on the animals' behaviour and give people a false sense of security.
People can be fined up to Aus$27,425 (US$20,700) for killing a crocodile, which are protected.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)