NSW Police were called to a break-and-enter at a logistics company at Port Botany after the security guard found a 27-year-old man among the shipping containers.
He was later arrested at the scene, but another man managed to escape.
After searching the area, police found a container from Italy packed with $60 million worth of cocaine in 1kg bricks stored within its walls.
Acting Superintendent Matthew Kennedy said they used a popular smuggling technique.
"They use legitimate containers, legitimate companies to piggyback and import drugs into Australia," Superintendent Kennedy said.
"They've [the companies] got no idea the organised crime syndicates are using them to put the prohibited drugs in to import into the country."
He said smugglers then attempt to break into the port and the shipping container before the drugs are detected.
On Thursday, the 27-year-old was charged with enter enclosed lands, assault, assault occasioning actual bodily harm and malicious damage.
But police said today that more charges were likely.
He has been refused bail and is due back in court on Tuesday, June 13.
On Saturday, a 19-year-old man was arrested in Leichhardt and 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 is due in court on Thursday, July 20, after also being refused bail.
It comes after three search warrants were executed across Balmain and Leichhardt, where police found items relevant to the investigation including crow bars, breaking tools, gloves and bags.
Police allege the men recently travelled from Athens, Greece, to access the drugs on behalf of local criminal associates.
Acting Superintendent Kennedy said drug syndicates are exploiting people to move drugs into the country.
"It is probably not the smartest thing for the organised crime group to send two Greek nationals who didn't know the English language, breaking into a port where they don't know the lay of the land."
He said there were corrupt insiders working in the logistics industry, but had a warning to criminals.
"They're going to get caught. We're going to arrest them, we're going to find their drugs, seize their drugs and they're going to go to jail."