He is also facing three charges of manufacturing the drug along with others.
Bowker was remanded in custody until later this month when he will appear alongside others arrested in yesterday's raids.
Forty-nine-year-old Waikato man David Gerrard O'Carroll was also due to appear today on three charges of manufacturing methamphetamine with others and one of possessing caustic soda.
But the court heard he was still in Auckland Hospital recovering from dog bites suffered in his capture by police and the court may go to his bedside tomorrow.
Police said he escaped when a search warrant was executed. He was captured less than two hours later, when he suffered "minor dog bite" injuries.
A police statement says the Operation Genoa raids also led to the seizure of five properties, more than $2 million in cash, gold bullion, silver ingots and a 30-foot launch.
Organised and Financial Crime Agency New Zealand (OFCANZ) Detective Inspector Bruce Good said 29 search warrants were executed at properties in Auckland, rural south Auckland and Nelson.
"A substantial amount of methamphetamine was recovered at a rural property in Miranda 80 kilometres south-east of Auckland."
The eight suspects arrested will face a range of charges including manufacturing methamphetamine, money laundering, unlawful possession of a restricted weapon, obtaining a false documents and participating in an organised criminal group.
Two of those apprehended were senior patched members of the Head Hunters gang.
Mr Good said the group were running a sophisticated methamphetamine manufacturing operation.
"We believe the suspects, many of whom have family connections, were using several addresses and storage units in Auckland, rural South Auckland and Nelson to produce, store and distribute methamphetamine and the Class B drug ephedrine," Mr Good said.
"Our intelligence indicates they were producing in excess of $1 million worth of methamphetamine at a time which gives an indication as to the size of the market they were supplying."
"In total we have recovered approximately half a kilogram of methamphetamine and 6 kilograms of precursor drugs and chemicals during Operation Genoa. This would have a combined street value of in excess of $3.5 million."
The seizure of significant assets such as luxury cars, gold bullion and properties in Auckland, rural south Auckland and Nelson was particularly satisfying, Mr Good said.
"Operation Genoa sends another powerful message to the criminal community that police will use every legal avenue at our disposal to target organised crime in New Zealand."
The head of the police inquiry says the methamphetamine market is as large as ever.
Detective Inspector Bruce Good spoke at a press conference this afternoon to reveal the haul from Operation Genoa including $2 million in cash, drugs, guns and false identities.
Asked how the size of the methamphetamine manufacturing syndicate linked to the Head Hunters compared with previous busts, Mr Good said it was difficult to compare police investigations.
However, he said the demand for drugs was substantial and isn't "going away''.
"My staff and I go by what is the market is telling us. What's the cost of the drug on the street, is it available, is it not? Nothing has changed over the years. That suggests to me, that the market is substantial, is still there and isn't going away,'' Mr Good said.
"Let's not kid ourselves. These aren't the only people manufacturing. That concerns me. The size of the market is large. That concerns me. The stress and strain on puts on our health system, our mental health system, and everything else that flows from that. That concerns me.''
