The Trump administration ordered several federal agencies to cease communication with the public, and in some cases halt new activity, in a move that raised fears about government work being done behind closed doors and about possible disruptions to programs.

The Environmental Protection Agency, the Department of Agriculture and the Department of Interior are among the agencies reportedly facing at least temporary gag orders, as the new administration takes over and begins what is expected to be a dramatic remaking of policy and an easing of environmental regulations.

In addition, the EPA was directed to freeze all new contracts and grants for outside organizations. The agency spends billions of dollars on fighting pollution, cleaning hazardous waste sites and conducting research on such topics as climate change. California gets about $180 million annually just to implement the Clean Water Act and the Safe Drinking Water Act.

While top federal offices commonly see restrictions when department leadership changes hands — allowing time to re-evaluate the mission and set new priorities — the limits enacted since President Trump took office Friday appear to go beyond the norm.

“There’s necessarily going to be some sort of pause, but I haven’t heard of a communications chill of this nature before,” said David Snyder, executive director of the First Amendment Coalition, a nonprofit group in San Rafael that advocates for open government. “If agencies are being ordered not to talk to the public about what they’re doing, how is the public to know what is going on and how can the public hold these agencies and individuals accountable?”

Much of the work facing censure appears to be related to the environment. Trump, who has called climate change a hoax and is a critic of water and air regulations, inherited an executive branch that sought to aggressively address global warming under President Barack Obama. Trump has pledged to do away with Obama’s climate policies.

EPA employees were told shortly after the inauguration, in an email first reported by online news site ProPublica, that all contract and grant awards were to be immediately suspended. It was not clear whether the directive applied only to new business or to existing work as well.

Jared Blumenfeld, who retired last year as the EPA’s Pacific Southwest regional administrator, called the freeze on contracts unprecedented and “chilling” for the agency and for communities that receive millions of dollars annually from the federal government.

Depending on how long it lasts, he said, the freeze could cut off as much as $5 million a year provided by the EPA to environmental nonprofits and other contractors doing everything from trash and pollution cleanup projects in San Francisco Bay to wetlands restoration along the shoreline. A total freeze in contracts would mean cleanups at toxic Superfund sites — including 23 in Santa Clara County polluted by the semiconductor industry — would have to shut down.

Many Superfund sites, like the Iron Mountain Mine, a shaft near Redding that spews acid-laced water, get more dangerous when it rains, Blumenfeld said.

“The two things that would keep me up at night when I was administrator was making sure the funding continued and high-rain events,” he said. “This is really a perfect storm of funding being cut and high-rain events, so it’s very worrying.”

David Lewis, executive director of Save the Bay, which has often contracted with the EPA to fund projects in San Francisco Bay, said he is baffled by the order.

“Of course, given other things this president has said and done, I think that there is legitimate concern that it could be politically motivated, not financially motivated,” Lewis said. “The EPA’s work is to protect our safety on a daily basis, so of course it’s concerning.”

Myron Ebell, who oversaw the EPA transition for Trump, told ProPublica that freezing “regulations going forward, contracts, grants, hires” enables the agency to ensure that policies will be consistent with the new administration’s direction.

Trump has nominated Oklahoma Attorney General Scott Pruitt to lead the EPA. Pruitt, who enjoys strong backing from fossil fuel companies and fought Obama’s Clean Power Plan in his home state, has criticized the agency for its heavy hand. His conservative allies expect him to ease regulation.

The EPA’s press office declined to comment on policy changes, offering only an emailed statement.

“The EPA fully intends to continue to provide information to the public,” the statement said. “A fresh look at public affairs and communications processes is common practice for any new Administration, and a short pause in activities allows for this assessment.”

An internal EPA memo recently leaked to the public, however, directed the agency’s communications staff to cease with press releases as well as social media and blog posts.

The office’s Twitter account, usually active, hasn’t released a post since before the inauguration, and its leadership blog was last updated by agency Administrator Gina McCarthy the day before Trump took office. In her post, she defended the office’s successful litigation of polluters.

“EPA under President Obama’s leadership has a remarkable success story to tell,” she wrote. “My hope is that our record will remind people that government can and does work for them.”

The Department of Agriculture has also instituted a communications lockdown on its science arm, the Agricultural Research Service, according to an internal memo first obtained by online news site BuzzFeed.

Michael Young, the USDA’s deputy administrator, wrote Tuesday that the gag order applies only to policy-related statements in press releases and interviews. He told the Washington Post that food safety announcements and peer-reviewed research papers are allowed.

The gag orders followed the weekend retweet by the National Park Service of pictures comparing President Trump’s inauguration unfavorably to President Barack Obama’s in 2009. The tweets were removed followed by a Park Service apology.

Then, on Tuesday, a series of tweets from the Badlands National Park account, @BadlandsNPS, highlighted studies showing record amounts of carbon dioxide in the atmosphere, ocean acidification and other signs of climate change. The tweets, which were soon removed, were celebrated online for their apparent defiance, receiving the hashtag #Badasslands and prompting fans to dub the park “Breaking Badlands” after the TV show “Breaking Bad.”

White House p ress s ecretary Sean Spicer said at his daily briefing Tuesday that he did not know about any restrictions on communications at the agencies, and would look into the matter.

Kurtis Alexander and Peter Fimrite are San Francisco Chronicle staff writers. Email: kalaexander@sfchronicle.com, pfimrite@sfchronicle.com Twitter: @kurtisalexander @pfimrite