A 15-year-old boy who was among a group of five people charged by counter-terrorism police following raids in Sydney has been known to police for several years.

Police allege the teenager and a 20-year-old man are associates of those responsible for the murder of New South Wales Police employee Curtis Cheng in October.

The pair were arrested this morning after Australian Federal Police (AFP) and New South Wales Police carried out the raids as part of Operation Appleby.

Another three people — men aged 21, 22 and 22 — were charged this afternoon with conspiracy to conduct an act in preparation for a terrorist act.

They were already in custody, after being arrested during earlier raids under Operation Appleby.

The 20-year-old is Ibrahim Ghazzawy from Raby. The teenager cannot be named for legal reasons but is from Georges Hall.

The boy faced court today and a decision on bail will be made in the morning.

He is a student at Bass High School, in Bass Hill in Sydney's west, the ABC understands.

It is believed the 15-year-old terror suspect arrested in counter-terror raids in Sydney this morning attends Bass High School at Bass Hill in Sydney's west. ( ABC News )

It is believed the Department of Education contacted law enforcement agencies to discuss a concern he was radicalising other students within his school.

Today's raid was the third he had been a target of. His home was raided in 2013, again in December 2014, and today.

He was home alone in the first raid, where documents, laptops and his Playstation were seized.

In the second raid, the boy was arrested and he was subsequently charged with possessing an unauthorised firearm.

A spokesperson for New South Wales Education Minister Adrian Piccoli said his office was made aware of the student's arrest.

The Education Department is working closely with the school.

AFP Deputy Commissioner Michael Phelan said painstaking analysis of documents seized in December 2014 raids led to the charges.

He said the documents mentioned the AFP headquarters.

"The planning documents were evolving. There's one mention of AFP building but they get the address wrong," he said.

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Deputy Commissioner Phelan said the charges related to activity when the teenager was 14.

He said police did not believe the plot was motivated by a directive from Islamic State (IS) militants.

NSW Police Deputy Commissioner Cath Burn added: "He was a part of the conspiracy, so in terms of the preparation and planning with the material that was being presented, we don't know exactly what his role would have been."

She said she was not aware of a link between the teenager and Farhad Jabar Khalil Mohammad, the 15-year-old who shot and killed Mr Cheng earlier this year before being killed in a shootout with police.

"I am not aware of a direct connection between the two 15-year-olds, however, the people who were involved with the murder of Curtis Cheng are associates of these people," Deputy Commissioner Burn said.

"We conducted search warrants last year on December 18 and we put people before the court on December 23 — and this is related to that particular matter.

"Some of the people we're charging today faced court on December 23."

Police said there was no new threat.

A 20-year-old man was arrested in terrorism raids conducted in Sydney on Thursday. ( Supplied: NSW Police )

'Radicalised to the point of acting out with violence'

Deputy Commissioner Burn said police had had a lot of contact with the boy's school in a bid to "prevent radicalisation before it gets to the point where people decide to act it out in violence".

A property at Bankstown, in Sydney's south-west, that was raided today ( ABC News: Kathryn Ward )

"A lot of the people we are dealing with ... are clearly radicalised to the point of talking about and acting out with violence," she said.

"How they've become radicalised, we don't actually know.

"We don't know how the 15-year-old has got to the point where we will allege he got."

There were also raids made in Bankstown, Wiley Park and Merrylands this morning.

Operation Appleby is aimed at detecting and preventing terrorist attacks on Australian soil.

In last year's raids, 15 people were arrested.

An alleged plot to kidnap and behead a member of the public was uncovered as part of that operation.