"It's shrinking," he said. "It gets physically smaller as it loses genes.
"The Y-chromosome can theoretically lose chunks at a time - 50 genes, 100 genes - depending on how big the deletion is."
Dr Waters said that when these genes were lost, the function they played also disappeared.
But genes would only be lost from the Y-chromosome if they no longer had a function of importance for males.
"If they do have some sort of male-specific role, such as in sperm production, they will be retained," Dr Waters said.
The ANU researchers found that a marsupial's Y-chromosome is genetically denser than the human Y-chromosome, meaning that animals like the tammar wallaby are bounds ahead on the "manliness" scale.
But Dr Waters said size in this case did not matter.
DNA samples from tammar wallabies and found more genes on the male chromosome than expected.
"There were lots of genes that we weren't expecting to find," he said.
"These genes have been lost from the Y-chromosome in placental mammals like humans but, for some reason, they have been retained in marsupials.
"This means there are different rates of gene loss on the Y-chromosome across species."
And Dr Waters said there was no risk of men becoming extinct.
"Y-chromosomes have been completely lost in other species, such as in some rodents, and genes important for male development have moved somewhere else in the genome," he said.
"The master switch that turns on male development can change and move around the genome, but the result will remain the same.
"Men will always be men, irrespective of the size of the Y-chromosome."
