About 94% of the employees of the Environmental Protection Agency (EPA) have been sent on leave of absence as part of the US government shutdown.

Nearly all of the agency's 16,205 employees across the country, with oversight of air quality, industrial waste, water and sewage treatment plants, have powered down their computers, updated their voicemail, filled in their last timesheets, and left buildings as part of the shutdown.

Only 1,069 essential staff – such as emergency personnel who deal with events posing an "imminent threat to human life" such as chemical spills or rail derailments– remained on duty. A few workers also stayed behind to feed lab animals, and water test plants.

EPA officials said the shutdown would disrupt monitoring of air and water quality.

It could also set back the agency's efforts to advance Barack Obama's climate change agenda.

Employees are barred from checking government email, using government-issued cellphones during the furlough, or catching up on any of their work for the duration of the shutdown.

"It stinks," said John O'Grady, a union representative at the EPA's Chicago office. "No one is going to be out inspecting water discharges, or wet lands. Nobody is going to be out inspecting waste water treatment plants, drinking water treatment plants, or landfills – nothing. None of that is going to be done. The employees are absolutely devastated."

He said most employees at the EPA had already lost about six days' pay due to leave since last April, and pay scales have been frozen since 2010.

The EPA is a prime target for the Republicans in Congress, who precipitated the government shutdown, because of its moves to limit the greenhouse gas emissions that cause climate change.

EPA officials had warned earlier that a shutdown could hurt Obama's climate change agenda. The agency was about to roll out new rules for promoting the use of biofuels, and tougher penalties against polluters.

The EPA was also working to set the first limits on carbon pollution from power plants – the pillar of Obama's climate change agenda. Those rules are still on course for release in June 2014 – but some Republicans on Tuesday still cheered the prospect of a shuttered EPA.

"There is some good news out of the shutdown, the EPA can't issue new regulations," Marsha Blackburn, a member of Congress from Tennessee, said on Twitter.

But EPA officials said there would be growing risk to public health if the shutdown lasted beyond a few days.

"It's like most of the other agencies. In the short term, the impact may not be terribly big, but over the long term, there is a cost to the work not getting done," said Jonathan Schweitzer, an environmental engineer at the agency and a veteran of the 1990s shutdown.

During the last shutdown, his team was forced to call off a planned inspection at a sewage treatment plant in the Chicago area. "During that time the treatment plant violated its discharge limits," he said. "In the long term if we can't review permits and pre-treatment programmes, then states and municipalities will likely tend to slack off if nobody is keeping after them as far as their job is concerned protecting the waterways."

Other environmental agencies are being affected by the shutdown – but only Nasa, the lead US government agency for climate science research, is taking a bigger hit than the EPA.

Just 3% of workers at Nasa remained on the job after Tuesday's shutdown. Nasa's website and Twitter feed, like those at other agencies, were also down.

But mission control for the six US astronauts at the international space station remained open, the agency said.

About half of the National Oceanic and Atmospheric Administration has been sent home without pay – mainly those dealing with climate change and oceans.

Hurricane spotters will stay on the job – the season runs through 30 November – but tornado watchers have been sent on leave, Climate Central reported.

Yosemite and other national parks and monuments were shut down, as was the panda cam at Washington's National zoo, as 81% of workers at the interior department were furloughed.

The Department of Energy (DoE) also sent 69% of its workers home, closing down research and energy efficiency programmes. Workers in charge of nuclear materials remained on the job, and so have staff at some of the DoE research labs for now.