UPDATE: 16×9 investigation into the use of a group of pesticides called neonicotinoids

WATCH ABOVE: 16×9’s investigation into the use of group of pesticides called neonicotinoids (NNIs)

A story 16×9 originally aired last fall showed how one of the largest manufacturer of nenonics, Bayer CropScience, continues to sell Clothianidin, a pesticide used on millions of acres of crops, even though the company has yet to prove to regulators that it is safe for bees. Bayer says that, when used properly, their product is does not harm bees.

Since then, a new study, published in the British Ecological Society’s journal Functional Ecology, found that these pesticides also appear to be harming the bee population’s ability to gather food.

Now, Ontario’s agriculture ministry intends to restrict the use of neonicitonoids, making it the first province in Canada to do so. The government will soon require farmers and other commercial growers to apply for permits, having a licensing system in place by the fall.

WATCH BELOW: Jim Coneybeare tells 16×9 his bees are dying at an alarming rate.

Jim Coneybeare believes a group of pesticides called neonicotinoids (NNIs) are killing his bees. Over the past three years, Canadian beekeepers have faced annual losses as high as 35 percent.

“Let’s face it, this is an insecticide designed to kill insects, and it’s doing that. It’s killing bees,” he says.

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Experts say these losses are unsustainable.

READ MORE: Garden centre flowers test positive for ‘bee-killing’ pesticide, study says

One-third of all food we eat – including almonds, melons, tomatoes, and cucumbers – is pollinated by bees. Beekeepers like Coneybeare just can’t keep up.

While there are many factors associated with bee declines – including mites, viruses, and loss of habitat – there is mounting evidence that NNIs, such as one manufactured by Bayer CropScience called clothianidin, play an important part.

When used appropriately, Bayer says its pesticide does not hurt bees.

“Currently there is no science that say otherwise,” says Bayer’s Ontario research-and-development manager Luc Bourgeois about the company’s production of clothianidin. Clothianidin is used widely on corn, soya, and other crops.

Read more: Bee deaths ‘a disaster in the making’

Bayer insists diseases and loss of habitat are the real threat and says its product is safe for bees. The company says it is making the product even safer by reducing bees’ exposure to it.

But a recent petition filed with Health Canada by a coalition of environmental groups, including the David Suzuki Foundation and the Sierra Club, claim that NNIs can be dangerous for bees. They submitted evidence from 19 peer-reviewed studies that concluded NNIs manufactured by companies such as Bayer harm bees, even at low levels.

“This is the time of year when bees should just be taking off,” says Christian Krupke, a Purdue University entomologist. Krupke believes NNIs have had a serious impact on bee health. “They should be doing fantastically well. To see hundreds of dead ones is not only strange it’s very…it’s the canary in the coal mine, so to speak. It’s a real warning that something is very wrong.”

READ MORE: Beekeepers propose class-action lawsuit over pesticide use

And regulators still don’t have all the answers about clothianidin.

Bayer submitted a study on the long-term effects of clothianidin on bees as part of the pesticide approval process in the mid 2000s.

Cynthia Scott-Dupree, a University of Guelph professor, was hired by Bayer to conduct a test as part of the approval process for the chemical. In her research, she set hives out in canola fields, some of which were treated with clothianidin. The results showed no long-term effect on bees from exposure to clothianidin on seed-treated canola.

Read more: EU bans pesticides in effort to save bees

But now both Health Canada and the United States Environmental Protection Agency (EPA) have asked the company to redo the study.

“I can’t understand why they would do that,” Scott-Dupree says. “Pressure – public pressure.”

Health Canada says it considers many of the findings of the study invalid “because of irregularities in how it was conducted.”

The agency says control- and test-hives were placed too close together, resulting in contamination of the controls.

Krupke agrees. “I would say if that’s the study that is used for the basis of registration…it would be insufficient.”

Health Canada has given Bayer until the end of 2015 to submit new research. By that time, the chemical will have been in use for more than a decade without a full understanding of its effects on bees.

And now, critics say the new science Bayer is expected to submit may also be flawed. The company hired Scott-Dupree again to conduct a $950,000 study. She says this study is improved from the one deemed faulty by Health Canada and the EPA.

“The first time we did it in 2005 there was some concerns about some of the results,” Scott-Dupree says. “So…we did it again and we tried to improve on all of the factors that were of concern the first time.”

Though her second study has not yet been submitted to regulators, she says the results are similar to what she found in her first experiment.

“We haven’t seen anything different than we did in the past. We’re not seeing massive colony losses.”

But Krupke says the design of the new study is “outdated, simplistic and uninformative.”

He says one of the problems is that Scott-Dupree did not start with hives and bees that were clean – with no exposure to pesticides before the experiment started.

WATCH BELOW: Cynthia Scott-Dupree, a University of Guelph professor, was hired by Bayer to conduct a test as part of the approval process for the chemical.

“If the hives aren’t clean, then everything is confounded. Then you don’t know what you’re going in with,” said Krupke. “You don’t have baseline data. How healthy were those hives? How stressed? How contaminated, if at all.”

“They were strong colonies. They produced a lot of honey the year before,” Scott-Dupree says. “They were choice colonies for this particular study. They all went into the study of equal strength.”

Other prominent scientists echo Krupke’s concerns.

Dave Goulson, a British bee expert, says pre-exposure to other chemicals “could add considerable noise to the data set, potentially obscuring any treatment effect.”

In a letter written to Health Canada in April, the Ontario Beekeepers Association urged the agency to put a moratorium on the approval of NNIs. “The preliminary results of this study, which are based on a serious flaw in the design, are not a basis for inaction on the part of regulators or policy-makers,” it added.

Critics also worry about a potential conflict of interest, citing Scott-Dupree’s ties to the industry. In July, she co-authored a study that looked at the effects of NNIs on bees in Canada. The study was co-written with David Drexler, a recently retired director of development and licensing at Bayer.

The paper downplayed the negative effects of NNIs, pointing out that the media had “practically ignored” bee death incidents that did not involve NNIs.

Scott-Dupree says her study was a review of a Health Canada database and that it showed that bee deaths caused by NNIs were mostly moderate to minor incidents. “There’s a lot of insecticides out there that you should be looking at as well if you’re going to try and start blaming chemicals for these losses.”

Scott-Dupree says that Drexler shares her views on this issue and that it is a “very balanced perspective.”

“I’m not saying I’m for or against neonicotinoids. In that particular study I am simply presenting the data in the way it appears in reports presented by the federal government.”

Health Canada is not expected to complete its review of clothianidin before 2018. Meanwhile, Ontario Premier Kathleen Wynne asked the federal government to expedite its review of NNIs.

But that may be too late for many beekeepers.

“The problem is bee keepers are finding it less and less profitable and more and more difficult to keep bees and are not necessarily willing to do it,” says Krupke. “So it’s not that we’ll have a collapse and we won’t have any bees; we won’t have beekeepers. And that is what in turn will lead to a shortage of bees, because it’s just too difficult to do the job.”

With files from Francesca Fionda and Megan Rowney