Rectangular holes in the stacks of paper inside many of the boxes had been cut to hide the drugs in.
Police estimated the ephedrine had the potential to make up to $150m of meth, otherwise known as 'P'.
A man who lived at an apartment off Queen St, who did not want to be named, said police arrested a Chinese man aged in his 30s outside the apartment today.
The man said police had observed the man for about two weeks in the lead up to his arrest, and had also watched CCTV footage that showed the man's movements.
"They were being very discreet, but were watching him for a couple of weeks," he said.
"They came in with a search warrant for an apartment today," he said.
Two apartments at the property were searched, with Customs staff also at the scene.
Officers from the Police Organised Crime team also carried out search warrants at residential addresses in Hillsborough, Ponsonby, Mt Roskill and Flat Bush.
They have arrested and charged three men, aged 31, 34 and 32 years old.
The men will remain in custody overnight and appear tomorrow morning in the Auckland District Court, on charges of importation of class B controlled drug (ephedrine) and possession of a class B drug for supply.
Each charge is punishable by up to 14 years imprisonment.
The arrests come a day after two Czech nationals were found with the largest-ever haul of meth to be smuggled through a New Zealand airport.
The 20kg of meth was found hidden in secret compartments in the bottom of two suitcases being brought into the country by two Czech nationals.
Customs said the pair arrived at Auckland Airport on a flight from Bangkok yesterday afternoon.
The Czech nationals were identified and questioned by Customs officers, and their luggage was searched.
The alleged smugglers are in custody and appeared in the Manukau District Court this afternoon charged with importing a class A controlled drug, which carries a maximum penalty of life imprisonment.
Customs official Jamie Bamford said criminal syndicates seeking to bring drugs into New Zealand would continue to be identified and prosecuted by Customs and partner agencies.
"We have sophisticated capabilities that are continuingly proving to work and deliver successes such as these. This seizure is a fantastic example of Customs' intelligence-led approach to risk management at the border and excellent work by our frontline officers," he said.
"Yesterday's seizure has prevented a significant amount of social harm to our communities, which is estimated at almost $25 million."
Auckland's organised crime policing head, Detective Inspector Scott Beard, said stopping the 200kg haul of ephedrine was significant in tackling the harm caused by meth.
"Though this is a great seizure and the circumstances seem like something out of a movie, the reality is there are families out there who are being destroyed by meth, kids who are growing up in contaminated homes and innocent people who are victims of serious crime as a result of this drug," he said.
"It is a truly awful drug and today is a great demonstration of law enforcement working together to target drug trafficking into our country."
