The 22-year-old allegedly drove into the CBD building's underground car park on Tuesday after telling guards he was there for an appointment, the AFP has confirmed.
The man walked around the building before getting into a lift with a counter-terrorism officer who confronted him when they got out.
Police officers allegedly found a knife on the man and a samurai sword in his car.
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He was charged with trespassing and other offences and faced Sydney's Central Local Court on Wednesday.
"An initial review of the incident indicates the breach of security protocols was caused by human error," the AFP said in a statement.
"The AFP has stringent security protocols in place for all its sites. These protocols are under constant review and are regularly adjusted according to risk assessments to ensure they are appropriate for the security environment.
"The safety and security of the community and AFP employees is always of the utmost priority.
"As a result an investigation into the breach is currently underway," it said.
The infiltration incident comes two days after five people, including a 15-year-old boy were charged over plotting a terror attack on the AFP's headquarters.
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