He did not seek name suppression and was remanded on bail - with strict conditions - until October 11.
The court was told that Thompson returned from Australia voluntarily shortly before his arrest.
Last week Detective Inspector John Sutton said Thompson's arrest was "significant".
The arrest was part of Operation Tiger, which is an ongoing operation to target the importation of psychoactive substances.
The investigation was initiated after Customs seized 1kg each of AMB-Fubinaca and AB-Pinaca, the psychoactive substances often used to make synthetic drugs.
Following this, police "worked in the background" and last month executed nine search warrants in Auckland, Palmerston North and Christchurch.
"Our most significant find was a storage unit in Rodney where 11kg of finished synthetic drugs were found and another 1kg of AMB-Fubinaca," Sutton said.
"The 1kg located by police and the 2kg by Customs would be sufficient to manufacture around 150kg of synthetic drugs, that's approximately 75,000, 2g doses of the drug, which is worth a street value of $1.5 million.
"The 11kg of finished synthetic drugs located in the storage unit would have had an approximate street value of $110,000."