The other men arrested face separate charges of belonging to a terrorist group.
The nine men are each charged with conspiring between June 2004 and November 2005 to carry out a terrorist act.
None of the suspects, who face a maximum penalty of life in prison if convicted, entered a plea, but their lawyers have said they are innocent.
The nine were charged with planning attacks in Australia's most populous city, Sydney.
|The men had allegedly considered an attack on |
Australia's only nuclear reactor [GALLO/GETTY]
No planned target has been revealed, but police alleged the suspects had Australia's only nuclear reactor, a small facility used to make radioactive medical supplies at Lucas Heights, under surveillance.
Prosecutors said at their pre-trial hearing that the nine suspects bought unrestricted chemicals that can be used in making explosives and downloaded from the internet instructions that included how to mix the cocktail of agents used to make the bombs used in the July 2005 London attacks.
The prosecutors alleged that the nine followed a Muslim cleric sympathetic to Osama bin Laden, and struck a pact to launch an attack because they felt their religion was under attack.
They had allegedly been urged by the cleric to inflict "maximum damage" in Australia for the sake of jihad.
The 18 men were arrested days after the government passed tough new anti-terrorism legislation making it easier for police to prosecute suspects involved in the early stages of planning attacks.
In separate development on Tuesday two Australian men were arrested in Melbourne accused of raising money for Sri Lanka's Tamil Tiger separatists.
Police said the men, who they said were not planning an attack in Australia, would appear in court for fundraising with knowledge that the money would be used to support the Tigers, which Australia lists as a terrorist group.