Police made the discovery after responding to reports of a break and enter at a shipping container logistics company about 11pm on Thursday at Port Botany.
A 27-year old man was arrested at the scene, while the other allegedly fled.
Specialist police took over the investigation under Strike Force Biles.
They found the drugs with assistance from Australian Border Force.
About 120kg of cocaine packaged in 1kg bricks stored within the walls of the container were discovered, worth a street value of approximately $60 million.
The 27-year-old was charged with enter enclosed lands, assault, assault occasioning actual bodily harm and malicious damage.
He was refused bail and will re-appear at Waverley Local Court on June 13.
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Detectives executed search warrants at three units across the Balmain and Leichhardt areas on Friday, where they found crow bars, breaking tools, gloves, bags and other items.
The items will undergo further forensic examination.
A 19-year-old was arrested during the search of a unit on Parramatta Road in Leichhardt.
He was charged with intent to commit indictable offence, large commercial supply of prohibited drugs and attempt to possess a commercial quantity of border restricted drug.
He was refused bail and will reappear at Downing Centre Local Court on July 20.
Police will allege the men had travelled from Athens, Greece, to access the drugs from the legitimate container on behalf of local criminal associates.