Green groups were among the loudest champions for the federal government’s sweeping ethanol mandate a decade ago, touting it as a near-magic fuel that could help ease a climate crisis.

But the Renewable Fuel Standard (RFS) that boosted ethanol use has fallen out of favor so badly that environmentalists now see themselves on the same side of the debate as Republicans such as Sen. Ted Cruz, arguing that the entire program is deeply flawed and must be completely overhauled.

The intense opposition to the RFS from environmental and conservation groups comes as the White House and congressional leaders work to craft the most serious reforms the program has seen since it was established more than 10 years ago. As Republicans and oil-industry groups bemoan the RFS as a job killer in the oil refining sector, environmentalists say their once-high hopes that ethanol could reduce carbon emissions, preserve land and help fight climate change have been proven wrong.

“The road to hell is paved with good intentions,” said Collin O’Mara, CEO of the National Wildlife Federation, a group that was once a vocal supporter of the RFS but now has become one of its chief opponents. “There’s a reason why [the RFS] was bipartisan, but the problem is that the law hasn’t been followed … We’ve distorted both our energy policy and our natural resources. That absolutely could’ve been avoided.”

Mr. O’Mara and other critics cite the fact that the RFS has mostly fueled wild growth in traditional corn-based ethanol, while the so-called “next generation” of biofuels — such as cellulosic ethanol — haven’t grown at nearly the same rate. Indeed, while the Environmental Protection Agency during the Trump administration has held steady the amount of corn-based ethanol that must be blended with gasoline each year, it’s reduced the mandated amount of advanced biofuels blending.

EPA Administrator Scott Pruitt last year said that was due to “market realities” that have shown it’s been harder to bring advanced biofuels, which are generally considered cleaner, into the marketplace than initially thought.

Many green groups have lined up behind legislation proposed by Sen. Tom Udall, New Mexico Democrat, and Rep. Peter Welch, Vermont Democrat, that would phase out the corn ethanol mandate portion of the RFS and reform the entire program into one focused on promoting advanced biofuels.

“Our bill is a forward-looking proposal, offering visionary reforms to put us on a cleaner and more sustainable path. The changes it would make represent a giant step forward to combat the urgent threat of climate change, cut pollution, and protect our planet for future generations,” Mr. Udall said last week.

The most ardent supporters of cellulosic ethanol and other advanced biofuels, however, contend that environmental groups have essentially partnered with the oil industry in an effort to undermine the future of ethanol, and that the Democratic legislation would be disastrous.

“When oil companies try to ghost write legislation for environmental front groups, you end up with some pretty backwards ideas, and that’s exactly what this appears to be. It’s dead on arrival with any lawmaker who cares about the climate, energy security, or the farm economy,” said Emily Skor, the CEO of Growth Energy, which represents biofuels producers.

Indeed, it appears unlikely the Udall-Welch bill will gain much traction in Congress. Sen. John Cornyn, Texas Republican, reportedly is crafting his own RFS reform package, and that’s more likely to attract support in the Republican-controlled Senate.

For the National Wildlife Federation and others, initial support for the RFS was based on the idea that corn ethanol would be little more than a stopgap as the next wave of biofuels were developed and put into widespread use. Their opposition, along with that of Mr. Udall and other RFS critics in Congress, stems from the fact that simply hasn’t come to pass, and they believe that a major overhaul of the RFS is now the only way to accomplish that long-term goal.

“A lot of folks on the Democratic side thought that by mandating more of the conventional food-based ethanols … that those would be a bridge to the second generation biofuels, but that clearly hasn’t happened,” said Rose Garr, campaign director at the environmental group Mighty Earth. “A lot of the climate benefits and carbon reductions were supposed to come from those fuels, and they just haven’t come online.”

The National Wildlife Federation contends, among other things, that the conversion of huge tracts of land into corn fields produces massive amounts of carbon emissions. More broadly, critics argue that the ethanol mandate promotes the continued use of fossil fuels at a time when the nation’s motor vehicle sector and other areas of the economy should be moving toward cleaner energy.

Green groups also say the creation of more corn fields has disrupted habitats and led to other serious conservation issues.

There’s conflicting information as to the true effect of ethanol on carbon emissions and, by extension, on climate change. While some studies have indeed shown that ethanol production can drive up carbon emissions, other research — such as a January 2017 study from the federal Agriculture Department — found that ethanol greenhouse gas emissions are 43 percent lower than gasoline, meaning that incorporating ethanol into the gas supply results in fewer emissions overall.

RFS opponents dispute that report, and the EPA hasn’t yet followed through on congressional mandates that it thoroughly study ethanol’s effects on the environment.

All sides of the debate, from lawmakers to the ethanol industry, have urged the EPA to complete its work.

Meanwhile, the ethanol industry — led by its largest trade group, the Renewable Fuels Association — counters that the overall land dedicated to growing corn has dropped since 2007, and that overall emissions in the transportation sector continue to decline.

Industry leaders also reject any reductions to the RFS, saying instead the program should be expanded and more ethanol allowed into the marketplace.

“We must change the narrative about renewable fuels so they are not viewed with cynicism and derision by key influencers and decision-makers,” Renewable Fuels Association President Bob Dinneen said in a recent speech. “We need to understand there’s another team on the field spinning their own anti-ethanol narrative.”