Two men in Victoria have been arrested for allegedly vandalising a culturally significant site on Taungurung Country.

The men have been accused of spray painting a rock face with graffiti at Paradise Falls in Victoria's Alpine National Park, which was discovered on May 12.

On Wednesday, Victorian Police arrested a 24-year-old man in Naarm's CBD, charging him with criminal damage and charges against the Aboriginal Heritage Act 2006.

The man was bailed to appear at Wangaratta Magistrates' Court on 29 September.

A second person, a 25-year-old male, was arrested by detectives on the Mornington Peninsula during a search warrant of his address and will be charged at a later date for the same offences.

The graffiti at the culturally significant site was approximately 10 metres wide and two metres high.

In a statement, the Taungurung Land and Waters Council (TLaWC) said they are "pleased" arrests have been made.

"Paradise Falls is a culturally significant site that is located on Taungurung Country, the statement read.

"TLaWC and Parks Victoria will remove the graffiti from the site with a focus on cultural sensitivity and healing, engaging with the Taungurung community in the process.

"TLaWC continues to work with Victoria Police and First Peoples State Relations during this investigation."

The graffiti is yet to be removed due to the ongoing police investigation, with specialist graffiti analysts from the Transit Divisional Response Unit assisting, Victorian Police said.