Australian Federal Police and NSW Police Force officers arrested a 24-year-old man in Merrylands and a 20-year-old in Bankstown on Wednesday morning as part of Operation Appleby.
"The message is that this in not a new threat we're dealing with," Police Deputy Commissioner Catherine Burn told reporters.
The counter-terrorism raids this morning are part of an ongoing police operation that has been focusing on a group of about 20 young men who police allege are committed to carrying out a terrorist attack in Australia.
"Today we have conducted a further two arrests, which brings this to a total of 13 people we will have brought before the court under Operation Appleby," Ms Burn said.
Police said the 24-year-old man is likely to be charged with making documents likely to facilitate a terrorist attack.
The offence carries a maximum of 15 years in prison if he is convicted.
Police said the 20-year-old man arrested will likely be charged with conspiracy to do an act in preparation for a terrorist act.
The apartment block which was one of two addresses raided in terrorism related charges in Sydney Source: AAP
If convicted, he could face life in prison.
New South Wales police will allege the Wooloomooloo navy base in Sydney was one of the locations intended as a target.
But New South Wales deputy police commissioner Catherine Burn said the arrests relate to events of last year and there is no fresh threat.
"We've conducted a number of disruption strategies and investigative strategies, and this has resulted in us arresting and charging 11 people with terrorism offences and related offences in regards to this alleged terrorist attack," she said.
"Today, we have conducted a further two arrests, which brings this to a total of 13 people we will have put before the court under Operation Appleby."
Both men are expected to face court later today.
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