The data shows methamphetamine is the most popular drug to import. A total of 360,646 grams was seized over the past year - that is heavier than the All Blacks front row.
It compares to the 1,080,315g seized in 2019-20.
MDMA imports also decreased, from 563,486g to 184,862g.
Customs investigations manager Bruce Berry said Covid-19 has impacted supply chains across a number of importation streams.
"It is a recognised impact of Covid-19 on the legitimate supply chain that is impacting the elicit at the same time.
"What we will see though is an increasing push of these products into our market as the world economies open back up."
Berry said the overarching picture was that organised crime will continue to exploit other avenues for importation such as fast and sea freight.
He said the constraints in the logistics of the shipping industry was also going to have an ongoing impact on the elicit as well as the legitimate drug supply chain.
"I think the decrease will be temporary and it's only a matter of time before the seizure data bounces back up."
Not all drugs have seen a decline in seizures over the past year
Synthetic cannabis seizures have increased by 339.3 per cent over the past year. A total of 8584g was seized in 2020-21 compared to 1954g in 2019-20.
Berry said he thinks this is due to a rise in the popularity of the drug.
"There is a range of products out there, between the different types of chemical elements being created around the world on a regular basis.
"I think it is exposure by New Zealand to synthetics and then the opportunities to make money off the back of that is what we are seeing."
Heroin seizures are also up, at 415g over the past year compared to 156g the previous year.
Berry said they are on alert with the knowledge organised crime is "extremely agile and adaptable".
"We know that they look at their supply chain as a business model and they will be changing the way they operate so we've increased our screening presence at the border.
"We are looking at the seizure data but certainly we're seeing increasing scale and sophistication of drug seizures, we've been seeing that for some time."