It was seen as one of the most distressing effects of climate change ever recorded: polar bears dying of exhaustion after being stranded between melting patches of Arctic sea ice.

But now the government scientist who first warned of the threat to polar bears in a warming Arctic has been suspended and his work put under official investigation for possible scientific misconduct.

Charles Monnett, a wildlife biologist, oversaw much of the scientific work for the government agency that has been examining drilling in the Arctic. He managed about $50m (£30.5m) in research projects.

Some question why Monnett, employed by the US Bureau of Ocean Energy Management, Regulation and Enforcement, has been suspended at this moment. The Obama administration has been accused of hounding the scientist so it can open up the fragile region to drilling by Shell and other big oil companies.

"You have to wonder: this is the guy in charge of all the science in the Arctic and he is being suspended just now as an arm of the interior department is getting ready to make its decision on offshore drilling in the Arctic seas," said Jeff Ruch, president of the group Public Employees for Environmental Responsibility. "This is a cautionary tale with a deeply chilling message for any federal scientist who dares to publish groundbreaking research on conditions in the Arctic."

The group filed an official complaint on Monnett's behalf on Thursday, accusing the government of persecuting the (PDF) scientist and interfering with his work. It seeks his reinstatement and a public apology.

Monnett was on a research flight tracking bowhead whales, in 2004, when he and his colleagues spotted four dead polar bears floating in the water after a storm. The scientists concluded the bears, though typically strong swimmers, had grown exhausted and drowned due to the long distances between patches of solid sea ice. It was the first time scientists had drawn a link between melting Arctic sea ice and a threat to the bears' survival.

Two years later, Monnett and a colleague published an article in the science journal Polar Biology, writing: "Drowning-related deaths of polar bears may increase in the future if the observed trend of regression of pack ice and/or longer open water periods continues."

The paper quickly heightened public concern for the polar bear. Al Gore, citing the paper, used polar bear footage in his film Inconvenient Truth. Campaigners focused on the bears to push George Bush to act on climate change, and in 2008, the government designated the animal a threatened species.

It was the first animal to be classed as a victim of climate change.

In 2010 the Obama administration began an investigation into his work. The scientist was suspended with pay on 18 July. He is said to be under a gagging order and forbidden from communicating with his colleagues. The employee group's complaint alleges that the investigation is a thinly veiled attempt to disrupt scientific work on the Arctic.

Oil firms, which want to drill in the pristine environment of the Chukchi and Beaufort seas, have been complaining of delays caused by environmental reviews. This month Obama issued an order to speed up Arctic drilling permits.

A spokeswoman for the Bureau of Ocean Energy Management Regulation and Enforcement (Boemre) said the government would continue to carry out research on the potential impacts of Arctic drilling, despite Monnett's suspension.

"All of the scientific contracts previously managed by Mr Monnett are being managed by the highly qualified scientists at Boemre," Melissa Schwartz said in an email. She noted that the investigation was being overseen by the inspector general, which is independent, and that it was being conducted according to the Obama administration's new guidelines on scientific integrity.

However, Peer argues the exercise is intended to discredit Monnett's brief paper on the polar bear.

Other organisations also accused the government agency of a long record of meddling in science. A 2009 report by the Government Accountability Office found huge gaps in Boemre's research on the impacts of drilling in the Arctic. And the Alaska Wilderness League stated: "Alaska Boemre has continued to ignore science and traditional knowledge in its decision-making about oil and gas development."

Documents posted on the League's website include a transcript of a conversation between investigators and Jeffrey Gleason, another government scientist on the 2004 trip. Gleason, who works for the government, in the Gulf of Mexico, said he did not necessarily share Monnett's conclusions that the polar bears were killed as a consequence of climate change. "It's something along the lines of the changing environment in the Arctic," he was quoted as saying.