Security at Melbourne Cricket Ground will be ramped up after two men were charged over smuggling handguns and bullets into a crowd of over 82,000 Australian Rules fans, police said Friday.

Victoria police said they arrested the duo, both in their 20s, after they refused to leave the stadium during Collingwood's defeat of Carlton on Thursday night.

A police search allegedly revealed the pair were each carrying a handgun and bullets, with one of the weapons already loaded.

Both men were charged with multiple offences, including possessing an unregistered handgun and ammunition without a licence.

Police said the incident was not linked to terrorism and there was no ongoing threat to the public.

"Last night's incident is extremely disappointing and upsetting," Melbourne Cricket Club chief executive Stuart Fox, who manages the stadium, said in a statement.

Despite security screening initially "identifying items of concern", a "breakdown" in further searches allowed the pair to enter the busy stadium, Fox said.

He added that security at the stadium would increase the "extensiveness" of manual searches, warning fans to expect delays entering the ground.

National broadcaster ABC reported that an AI-powered screening system had initially flagged the pair, but human error meant the alert was not followed up effectively, allowing the men to enter.

Security had reportedly tried to kick the men out of the ground due to bad behaviour but had to call the police when the men refused to leave, leading to the discovery of the weapons.

"This is pretty shocking," Australian Prime Minister Anthony Albanese told a Sydney radio station.

"I hope that they (the men) get the book thrown at them for this. And I do want to thank Victoria Police for their work in keeping people safe."