Laws that kicked in from July saw vapes only allowed to be sold in pharmacies, with bans also applying to the product being imported into Australia.
Health Minister Mark Butler said almost three months from the ban being implemented, some stores were continuing to sell the product.
"It's quite clear that some convenience and tobacconist stores are breaking the law," he told ABC's Insiders program on Sunday.
"We've taken the approach in the first few months to try to get businesses to surrender their vapes, and many businesses have done that ... but we are going to have to switch to, I think, a far more assertive approach."
Health Minister Mark Butler says the crack down is critical for the protection of young people. (Jane Dempster/AAP PHOTOS)
Penalties of up to seven years in prison and fines of $2 million apply for those illegally supplying or manufacturing vapes.
Mr Butler said while the laws had been working for reducing access to vapes, there was still a long way to go.
"I never pretended that this would shut down (vaping) overnight," he said.
"Vapes were presented as a therapeutic good to help hardened smokers kicked the habit, but we learned very quickly that that was not what it was about. It was actually about recruiting a new generation to nicotine addiction."
More than five million vapes have been seized at the border since a ban on imports kicked in from January.
The health minister said the crack down was critical for the protection of young people.
"I want to see prosecution starting to be prepared by authorities, because this is too important to the health of our young people," he said.
"So it's not going to happen overnight ... but I'm determined to keep fighting this and protect the health of our younger Australians."
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