The Herald Sun published the cartoon on Tuesday with blurred-out areas across her breasts and hips.
"From the Commonwealth Games cancellation collection ... the premier's new clothes," the caption reads.
The cartoon by Mark Knight mimics the Emperor's New Clothes, a Hans Christian Andersen folktale often used to point out an obvious truth.
The premier said she did not recall any male politicians being depicted in such a manner.
"It's 2023," Ms Allan told reporters.
"It's pretty reasonable to expect that the Herald Sun in-house cartoonist should be able to draw women without using sexualised imagery.
"They've done that. It's a matter for them."
As the former minister tasked with delivering the 2026 Commonwealth Games, Ms Allan has faced scrutiny over the lead-up to Victoria's decision to cancel the event.
Mr Knight insisted he didn't draw the cartoon for the sake of depicting a naked premier but rather to reference the folktale and evidence given at a parliamentary inquiry into the cancellation of the Games on Monday.
"It's not sexualised imagery," he told ABC Radio Melbourne.
"I felt that some of the information that was coming out left the premier a little bit exposed and my cartoonist brains clicked into gear and it was fashion week and, I thought, 'well, this is not a bad idea'."
Mr Knight pointed to his past work drawing former prime minister Tony Abbott in budgie smugglers and a scantily-clad Opposition Leader Peter Dutton spearing a boat emblazoned with "the voice" as proof of him practising equal opportunity mockery.
The Walkley Award-winning cartoonist courted global controversy in 2018 for his depiction of tennis legend Serena Williams throwing a tantrum during that year's US Open final.
"There's nothing worse than a boring cartoonist ... but I don't seek to deliberately outrage," he said.
Ms Allan became Victoria's first female premier in more than three decades last month, replacing Daniel Andrews.
In his almost nine years in the top job, former Victorian Labor premier Steve Bracks said he was never subjected to the "awful, sexualised treatment" Ms Allan had faced in less than a month.
"We need to do better," he said in a statement.
Victoria's inaugural Public Sector Gender Equality Commissioner Niki Vincent said she found the cartoon tiresome and suggested it used sexism.
"This is another example of how to make fun of a woman leader using their body," Dr Vincent told ABC Radio Melbourne.
Deputy Premier Ben Carroll said he hadn't seen the cartoon but recalled Australia's first female prime minister Julia Gillard's speech after she was deposed in 2013, declaring she was confident it would be easier for the next woman.
"In 2023, to be going through that sexualised imagery, that misogynistic-type betrayal is just not on."
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