The company's Simon Kenin said in a blog post that the website appeared to have been compromised due to a flaw in the Drupal content management system with which it was built.
He said he found that the website which was hosting the mining script was one that had been exploiting the flaw in Drupal since May.
As iTWire reported in May, a security researcher had warned about mining for the monero cryptocurrency being carried out through spreading a script for the same.
About 450 Australian Government sites run a customised version of Drupal known as govCMS which has been built by the Boston-based open source firm Acquia.
"Although the campaign has been updated several times since May, many website owners didn't update their Drupal version in a timely fashion," Kenin said. "This allowed cyber criminals to compromise their websites to mine cryptocurrency."
He said he had tried several times to contact the Make A Wish foundation but received no response. However, the script had been removed from the site soon after the efforts to contact them began, he added.