He told Parliament on Monday that the networks of the Liberal, National and Labor Parties had also been breached and that security agencies were working on bolstering defences.
Morrison said there was no evidence of any danger to electoral systems and that the Australian Cyber Security Centre was across the task of beefing up security.
He said the ACSC's resources would be available to all political parties in the run-up to the federal election which is expected to be held in May.
In 2011, the network was breached by attackers who were said to be from China and its defences were upgraded thereafter.
Morrison said there was no proof there had been any attempt at electoral interference, but said the Australian Electoral Commission was being advised and all political parties would be provided support if needed.
“Let me be clear ... there is no evidence of any electoral interference,” he said.
“We have put in place a number of measures to ensure the integrity of our electoral system. I have instructed the Australian Cyber Security Centre to be ready to provide any political party or electoral body in Australia with immediate support, including making their technical experts available.
“They have already briefed the Electoral Commission and those responsible for cyber security for all states and territories. They have also worked with global anti-virus companies to ensure Australia’s friends and allies have the capacity to detect this malicious activity.
“We have acted decisively to protect our national interests.”
David Higgins, technical director for security firm CyberArk in the EMEA region, supported the conclusion that a nation state was involved.
“Whenever something of this nature affects a political party, nation state involvement must be considered as likely, given what has been reported," he said in a comment after Morrison made his statement.
"While the motive is not yet clear – and motive is, of course, key in determining who might have accessed these systems – the fact of who has been targeted and the level of sophistication involved indicates some kind of nation state involvement or sponsorship."
Higgins said often the objective was to gain competitive market advantage – "government policies that could be seen as likely to provoke ‘trade wars’ are very likely to trigger a new round of nation-state attacks designed to steal intellectual property and other trade secrets".
"But this is just one of many potential reasons. Destabilisation, experimentation, information wars, policy influence and myriad other possibilities also exist.”