EPA employees have also been instructed not to release press releases, publish blog posts or post anything on social media. It's part of a crackdown by the new administration that seems to be especially felt at the EPA and the Interior Department, leaving some employees "terrified."
EPA spokesperson Doug Erickson said the objective of the website review is to have an agency page that reflects the new administration's policies.
"We are not passing judgment on science," he said.
Asked if climate change data on the EPA site would be removed because it doesn't reflect the ideas of the new administration, Erickson responded, "you can speculate that if you want but I didn't say that. I am only saying we are reviewing the website to make sure material on it reflects the new administration."
Trump was outspoken during the campaign about wanting to curb environmental regulations that he said were hurting businesses. The President has also been a known climate change denier, tweeting in 2012 that "the concept of global warming was created by and for the Chinese in order to make US manufacturing non-competitive."
White House press secretary Sean Spicer said there has been no specific directive to agencies. "There's nothing that comes from the White House," he said Wednesday.
But the first week of the Trump administration has seen various efforts that could stifle communication with the public.
The Interior Department's digital team was told to temporarily stop using Twitter after the National Park Service retweeted messages Friday that negatively compared the crowd sizes at Barack Obama's 2009 inauguration to Trump's inauguration.
Christine Todd Whitman, EPA administrator under President George W. Bush, said the moves are heavy-handed.
"I would say its extreme. Its an administration trying to put a strong marker down," Whitman said.
"The reason for what they are doing is reasonable," she added. Yet "when you put in context how they feel about the press, he doesn't trust the press, it makes Trump administration approach look extreme."
The lockdowns have led to widespread discontent inside government agencies that deal with climate change and environmental protections.
Career staffers at the Interior Department, which includes the Park Service, are "terrified" that their day-to-day operations could run afoul of the Trump administration's desires, a source with knowledge of the situation inside the government agency tells CNN.
Tensions are even higher after Friday's tweets, the source says, leaving many at the department feeling like they have to be extra careful as they go about their daily routines because it is unclear what could set off the White House or Trump's political appointees.
House Minority Leader Nancy Pelosi said reports of gag orders to the EPA are "just appalling" and that the Trump administration seems "to be happy to be in a fact-free zone."
Speaking to reporters in the Capitol Wednesday, Pelosi also addressed reports of efforts to take down climate change material on the EPA website, calling such activity a "deterioration of intellectual sources to prevent information to flow."
Jeremy Symons, a former career employee at the EPA who worked through the transition between President Bill Clinton and George W. Bush, said this sort of information lock down is "unprecedented."
"It didn't happen," Symons, who now works at the Environmental Defense Fund, said when asked whether anything like this happened during the Clinton-Bush transition. "This administration is walking into this transition... as though the impartial experts that keep the government running are political enemies and that is a mistake at EPA or any agency."
He added, "It bodes badly for what we should expect moving forward from here."
Trump agency websites are being closely watched both from both inside and outside the government.
Badlands National Park's official Twitter account tweeted statistics about climate change on Tuesday, drawing attention from Democrats and others opposed to Trump administration policies. The tweets were up for mere hours before they were deleted.
In a statement, the Park Service blamed "a former employee who was not currently authorized to use the park's account" for the tweets.
The change in social media since the last major presidential transition complicates things, said Joe Valenzano, associate professor and chairman of the Department of Communications at the University of Dayton.
"Because social media is relatively new, and the use of blogs to promote policy is relatively new there's no real precedent to say whether freezing communications in the way Trump administration has is a common practice or not," he said.
But "in the larger context of Trumps war on the media you see tapestry that makes it look somewhat strange."