Kiwi Bee Waikato hives were there on Friday and gone on Monday, leaving branch manager Harald Aalderink and staff gutted.

Thieves have all but cleaned out one Waikato bee keeping site, leaving apiculturists to wonder if the hives were stolen to order.

A weekend heist saw Kiwi Bee Waikato stripped of 50 hives from a Waipapa Rd site, southeast of Te Awamutu.

The situation is far from uncommon, says the National Beekeepers Association, and could be linked to the "manuka boom".

Stealing the hives would require specialist knowledge - and a suitable vehicle.

At the Kiwi Bee site on Monday morning, all that remained were empty pallets and one lonely hive.

"We felt really gutted," Waikato branch manager Harald Aalderink said.

"It's really a shock that the whole yard was cleaned out... You can't believe it."

The business is a Comvita subsidiary and produces manuka honey from about 8000 hives.

Aalderink thought the thieves would take the hives out of the region, possibly up north where the honey flow had started early.

"Sometimes we think they steal to order... You have to know what you're doing."

Each hive had just one box and no honey, but they're worth about $400 each and weigh about 20kg.

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Kiwi Bee is now considering security options such as cameras and GPS trackers.

It's not the first time the business has been targeted; about 60-80 hives were taken throughout 2014.

In one case the person opened the lids and selectively took frames from about 20 Te Kuiti hives, Aalderink said.

He thinks the boom in manuka honey could be behind increasing thefts - last season it sold for about $30/kg.

"There's so much money involved."

Anecdotal reports of "some sizeable thefts" of hives had filtered through to the National Beekeepers Association of NZ and it seemed they were increasing.

"This is not the first time by any means," chief executive Daniel Paul said.

He hadn't heard of stealing to order but said it wasn't impossible.

"The assumption is that most of these hives are being stolen because of the manuka boom," he said.

"The assumption is also that the people stealing these hives are beekeepers themselves because you're going to have to know what you're doing. It's not like just you or I can just rock up to 50-odd hives and nick them."

Thieves normally struck at night, and would have to go with a truck to transport their loot.

"All hives have to be registered. Unfortunately we can't track them through that because people who are nicking hives are not necessarily going to be open about what hives they've got."

The stolen Kiwi Bee hives would stand out because they had a distinctive groove below the handle for the barcode, Aalderink said.

"If we find them we can see straight away that they're our hives."

Anyone with information can call Te Awamutu Police on (07) 872 0100 or anonymously contact Crimestoppers on 0800 555 111.

Other recent beehive thefts

June 2015: Eight bee hives, worth $500 each, taken from Huntly

April 2015: 20 bee hives, worth about $6000, taken from Maromaku area in Northland.

March 2015: 20 harvest-ready hives taken from Uruti, about 50km north of New Plymouth