A Northern Territory beekeeper says about 1 million of his bees have been deliberately killed with an insecticide, in the second suspected poisoning of commercial bee boxes near Katherine in a year.

Sam Curtis found the dead bees inside and near their boxes on a track outside Katherine, a few kilometres off the Victoria Highway, in July.

Last week he received confirmation from a laboratory that the bees had died from Fipronil poisoning — an insecticide commonly used to kill termites.

The hives were about 5 kilometres from where another beekeeper had about 120 hives of bees die from the same insecticide in November.

Mr Curtis said the loss of bees would set his business back about $20,000.

"We had 100 breeding colonies that were completely decimated and we had probably 20 full-strength hives that were totally destroyed," he said.

"The rest were severely weakened, so we had to clean out the comb in the boxes so there was no [insecticide] residue affecting the brood rearing, so the bees can recover.

"Between all the hives it would be about 1 million bees [dead]."

Beekeeper Sam Curtis has asked the NT Police to investigate the incident. ( ABC Rural: Daniel Fitzgerald )

Mr Curtis has ruled out the bees being accidentally poisoned by insecticide use on a nearby mango farm because it was spraying a different chemical.

He suspected the person responsible for the poisoning was someone who "doesn't like bees".

"Some people reckon it could be greenies because they think that [European] bees attack the native bee colonies, so they would try and kill the European species," Mr Curtis said.

"Or it could be anyone related to the agriculture sector because Fipronil is a rather difficult chemical to come across."

Two mass bee poisonings may be linked

More than 10 months on from the mass poisoning of Nathan Woods's bees near Katherine, no-one has been held responsible and NT Police have closed their investigation.

Mr Curtis said it was possible the two cases were linked because they both occurred in the same area.

"Both of us like to put bees out that way for various trees, but our beehives aren't very noticeable from the road," he said.

"So this person obviously goes up and down [that track] regularly, if it is the same person."

In addition to the loss of the bees, Mr Curtis said he was reluctant to return his bees to what was one of his best locations to place his hives.

"We were trying to breed queen bees to replace some of the hives that were dying over the years for pollination; this has really screwed that up because that was our queening site," he said.

Mr Curtis said he had asked NT Police to investigate the deaths of his bees.