Environment Minister Nick Smith has been accused of blatant scaremongering as he moves to stop local councils from controlling genetically modified organisms (GMOs) in their districts.

Dr Smith said the government was acting because it was worried local councils would stop important medical trials that use GMO technology from going ahead, and the government was looking to change the law.

The High Court this week upheld the Environment Court's decision that local councils could have control over the use and release of the technology in their districts.

Farming lobby group Federated Farmers has been challenging the right of local councils to regulate GMOs in the courts.

Dr Smith said the government would now step in, because GMOs were effectively being regulated twice.

"Regulated by the Environmental Protection Authority under the Hazardous Substances and New Organisms Act and then regulated again by councils through the Resource Management Act," Dr Smith told RNZ News.

"What we are doing is saying that doesn't seem to work very well, particularly given the fact that we have no biosecurity controls between different councils."

Dr Smith said local councils did not have the necessary technical expertise to deal with GMOs, and that council bans could affect future medical trials.

"Well, the government is concerned at the implications in the new Auckland Unitary Plan that prohibit the release of GMOs and its impact on an important programme for liver cancer treatment at Auckland Hospital.

"As well as the future implications for a number of medicines that are increasingly using GMOs for treatment," Dr Smith said.

But councils with the ability to regulate GMOs say medical trials are specifically exempt.

Dr Kerry Grundy is the convenor of the inter-council working party on GMO risk evaluation. Dr Smith's claims were a total beat-up, he said.

"Right from the word go, our provisions were only aimed at outdoor use of GMOs - so releases of GMOs to the environment or field trials outdoors.

"The provisions specifically permit indoor research in contained facilities, laboratories, hospitals and medical applications involving GMOs."

In a statement, Auckland Council said it didn't agree that the Pexa-Vec vaccine - the liver cancer treatment being trialled - or any other medical applications or clinical trials, would be prohibited activities under Auckland's Unitary Plan.

The Green Party's genetic engineering spokesperson, Steffan Browning, said the Environment Minister was simply doing Federated Farmers' bidding, following its court losses.

"Nick Smith is definitely trying to scaremonger... Nick is using every emotive tool he can to push New Zealand down the genetic modification route," he said.

Despite repeated requests, Dr Smith's office hasn't provided the advice the minister said he received showing that medical trials would be affected.