The drugs allegedly arrived on a so-called black flight, where a light aircraft flies under the radar or turns off monitoring systems to avoid detection.
Australian Federal Police said the men are members of a transnational organised crime syndicate who handled practical arrangements to import 52 kilograms of meth.
"These men have not only allegedly imported a dangerous drug into Australia, but flying at low altitude without proper instruments poses a huge safety risk for other aviation aircraft," AFP Commander Kate Ferry told reporters.
Cmdr Ferry said the plane had been en route to NSW and had stopped in the central Queensland town of Monto to refuel.
Three of those charged provided ground support for the flight and had staged themselves in Queensland since February, the AFP said.
Police allege the syndicate's ringleader, a 40-year-old man from Wilton south of Sydney, took directions from more senior international crime figures and made direct contact with co-conspirators in PNG to organise the handover.
Two men, 54 and 40, allegedly helped with logistics including refuelling the aircraft and facilitating communications over a network of encrypted burner phones.
The other two men, 51 and 52, allegedly flew a twin-engine Beechcraft plane from Wilton to the town of Bulolo in PNG, more than 250 kilometres northwest of the capital Port Moresby.
Cmdr Ferry said the senior pilot has significant experience in the aviation industry and called off several previous attempts due to safety concerns.
The men are alleged to have collected the meth and concealed it in the plane's nose cone before returning to an airstrip in Monto where they were intercepted. In an effort to avoid radar detection, they allegedly flew at a low altitude with the transponder turned off.
AFP officers are continuing investigations into the origins of the drugs, in collaboration with law enforcement agencies in PNG and Southeast Asia.
Cmdr Ferry told AAP that methamphetamine imports to Australia mainly originate in Southeast Asia, particularly Myanmar where political turmoil has left a regulatory vacuum for organised criminals to exploit.
Officers raided four homes and businesses in NSW and found firearm parts, drug paraphernalia and documents referencing aircraft parts and travel to PNG.
Four of the five men appeared in the Bundaberg Magistrates Court on Wednesday and one is scheduled to appear on Thursday.
The men have all been charged with importing a commercial quantity of methamphetamine and face a maximum penalty of life imprisonment.
PNG police have also arrested a 42-year-old Chinese national, who is being questioned in relation to the matter.
NSW Police Detective Chief Superintendent Jason Weinstein said drug importation is central to the escalation in gang-related violence in NSW.
"To people who think that the deal they take on a Friday night at the pub is OK and has no consequences for families or the community at large - you need to think again," he said.
"You are all supporting organised crime in one facet or another."
In January, NSW police arrested four men as part of the biggest drug bust in Australia's history, seizing over two tonnes of meth worth almost $2 billion.
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