In addition, Mr Joyce said, many different organisation had come under attacks for months at a time in a bid to scoop up valuable intellectual property, business information or to get at their customers.
The principal targets of the global campaign were internet service providers, firms running critical infrastructure, government departments and large companies, the alert stated.
The warning is unrelated to the administration's recent military strikes on suspected chemical weapons facilities in Syria, action Russian Federation condemned.
While Australia did not take part in the strikes - the US, UK and France carried them out - Australia has been part of previous actions in Syria.
The announcement is the latest in a series of related moves by the Trump Administration, which in recent months has publicly blamed Russian Federation for launching the NotPetya worm that has been characterised as the costliest and most destructive cyber attack in history.
"The Foreign Affairs Ministers classified as shocking the alledged chemical attack in Syria and asked for an independent investigation", says Euronews reporter Isabel Marques da Silva.
Some private-sector cyber security experts have criticized the USA government for being too slow to release information about cyber attacks.
"These incidents are unacceptable and the Australian government calls on all countries, including Russian Federation, not to take actions that could lead to damage of critical infrastructure that provide services to the public".
While a significant number of Australian organisations had been affected, there was no indication Australian information had been compromised, he said.
In August it issued a warning saying that switches with Cisco Smart Install accessible from the internet, and routers or switches with simple network management protocol enabled and exposed to the internet, were vulnerable.
Washington and London have detailed how Russian-backed hackers have been compromising network devices around the world since 2015.
Advice circulated by USA and United Kingdom authorities warned Cisco routers - a common commercial brand - were affected.
British and United States intelligence services released a joint statement on Monday evening saying the main targets included "government and private-sector organisations", as well as providers of "critical infrastructure" and internet service providers. It included advice to companies about what they can do to protect themselves and warned specifically of attacks on routers, the devices that channel data around a network.
In a first-of-its-kind joint statement, released on Tuesday, the officials said they had "high confidence" that Russian state-sponsored cyber actors "are using compromised routers to conduct man-in-the-middle attacks to support espionage, extract intellectual property, maintain persistent access to victim networks, and potentially lay a foundation for future offensive operations".