Public interest groups and a labor union sued the government to block enforcement of the policy, saying it overstepped Trump's constitutional authority.
Judge Randolph Moss's comments during a hearing last week in U.S. District Court for the District of Columbia hinted at some agreement with arguments from attorneys for Public Citizen, the Natural Resources Defense Council and the Communications Workers of America.
Moss described the one in, two out policy as being "like a shadow regulatory process on top of the regulatory process."
Critics of the policy to eliminate two regulations for every new one say it limits government agencies in their ability implement environmental and safety standards that could protect the public.
"This policy was rushed and ill-advised," Rep. Jared Polis, D-Boulder, told Colorado Politics. "Although there are certainly some standards that could be reformed or repealed, 'one in, two out' is an arbitrary and blunt instrument that only serves to hurt taxpayers and Americans. Provisions that help protect our health and safety, our pocketbooks, jobs and so much more would be at risk."
The policy represents a special threat for Polis, a candidate for governor next year who advocates moving Colorado toward completely renewable energy sources by 2040.
Sustainable energy programs supported by government agencies would require more regulations.
"This 'one in, two out' policy will also make it more difficult to promote clean energy innovation," said Polis.
A better option would be to invest in energy sources that could be developed through the kind of federal labs and research institutions found in Colorado, he said.
"This policy makes drastic changes to provisions when we only need minor ones," Polis said. "This policy could also cripple our entrepreneurs and our research facilities."
President Donald Trump said shortly after he took office that he would like to eliminate 75 percent of federal regulations.
Government agencies instituted most of their regulations to carry out laws passed by Congress.
"This isn't a knock on President Obama," Trump said when he signed the executive order Jan. 30. "This is a knock on many presidents preceding me."
Trump instituted the policy to help industries avoid burdensome costs of regulation.
Previously, the government cost considerations were limited to each regulation separately. Now the agencies must determine which other unrelated regulations they will eliminate.
The advocacy groups' lawsuit says the president's executive order violates his duties under the "take care" clause of the Constitution and forces agencies into actions that will harm Americans.
Their lawsuit won support from Garrett Garner-Wells, director of the advocacy group Environment Colorado.
"The Trump administration's 'one in, two out' regulatory policy puts Colorado's health, safety and future in jeopardy," Garner-Wells said. "This policy is just one more giveaway to big polluters at the expense of Colorado citizens."
Rep. Ed Perlmutter, D-Arvada, was less harsh in criticizing the Trump administration policy but expressed concern about possible risks to the public.
"Reviewing and updating regulations over time makes sense," Perlmutter said. "The number of regulations is less important than establishing good policies and reasonable standards for public health, the environment and safety regulations and that help the hardworking people in the middle."
Justice Department attorneys and the attorneys general of 14 states that filed an amicus brief in the case argued the one in, two out policy merely continues the president's authority with executive orders under Article II of the Constitution.
The amicus brief added that states have been burdened with too many federal regulations.
"The result is a situation where agencies have implemented far more regulatory burdens than Congress ever envisioned," the brief says.
The Colorado attorney general did not join the amicus brief. A spokeswoman said Attorney General Cynthia Coffman was unaware of it.