At first glance, it’s a big step forward in curbing climate change. In a deal announced Thursday, the Biden administration and the airline industry agreed to an ambitious goal of replacing all jet fuel with sustainable alternatives by 2050, a target meant to drive down flying’s environmental toll.

As early as 2030, President Biden said, the United States will aim to produce three billion gallons of sustainable fuel — about 10 percent of current jet fuel use — from waste, plants and other organic matter, reducing aviation’s emissions of planet-warming gases by 20 percent and creating jobs.

The airline industry has set sustainable fuel targets before. The International Air Transport Association, a trade group of the world’s airlines, had pledged to replace 10 percent of the jet fuel it uses with sustainable fuels by 2017. That year has come and gone, and sustainable fuels are still stuck at far less than 1 percent of supply.

Could it be different this time?

It could. Momentum is building for action even in industries like aviation, which are particularly reliant on burning fossil fuels, because powering planes solely with batteries, especially for long-haul flights, is tricky.

But there’s a twist: Depending on the type of alternative fuel, using billions of gallons of it could hurt, not help, the climate.

Scientists’ concerns center on the complicated calculations that go into assessing the true climate-friendliness of biofuels, a major subset of sustainable fuels. Growing crops like corn and soy to be made into biofuels can significantly change how land is used, and trigger emissions increases — for example, if forests are cut down or grassland is dug up to make way for those crops.

Add in the emissions from fertilizers, and from transporting and processing the crops into fuel, and the overall climate costs become unclear. The Environmental Protection Agency estimates that corn ethanol emits just 20 percent less greenhouse gas emissions than gasoline, and that calculation doesn’t fully take into account past land-use changes, scientists say. Scientific studies have long shown that biofuels can be as polluting as fossil fuels.

Growing crops for fuel also competes with food production and strains water resources, according to scientists. And making fuels from waste, like discarded cooking oil, presents a far simpler challenge: There just isn’t enough old cooking oil available.

“Aviation fuels are going to be one of the toughest nuts to crack because electrification isn’t as simple” as electrifying, say, cars, trains or other ground transportation, said Jason Hill, professor of bioproducts and biosystems engineering at the University of Minnesota. “The problematic part is that today’s biofuels don’t reduce greenhouse gas emissions. That’s not where the state of the science is. They can actually make them worse.”

To address those concerns, the Biden administration says that it will help cut costs and rapidly scale domestic production of sustainable fuels, but in a climate-friendly way. The administration has proposed a sustainable-aviation-fuel tax credit that would require at least a 50 percent reduction in overall greenhouse gas emissions, a standard that would disqualify most crop-based biofuels. Congress is now studying the plan.

Corn and soy producers are pushing for a review of those requirements.

In a letter to members of Congress dated Aug. 6, major agricultural organizations including the American Farm Bureau Federation called for a redo of studies on the environmental impact of crop-based fuels. The groups also urged the Department of Energy to lead fresh studies into crop-based biofuels, rather than the E.P.A., the agency tasked with regulating greenhouse gas emissions.

“E.P.A.’s analysis does not reflect or capture the continuous improvement that has been witnessed over the past decade in biomass production or the technology and efficiency improvements in fuel production,” they wrote. The Farm Bureau did not immediately provide comment.

The groups’ demand appears to have been granted. A memorandum of understanding outlining the government’s sustainable aviation fuel effort says the Department of Energy will lead that analysis, and excludes the E.P.A.

“This certainly reads like a plan to promote crop-based biofuels in aviation,” said Dan Rutherford, aviation director at the International Council on Clean Transportation, a nonprofit that provides technical and scientific analysis to environmental regulators. “The E.P.A. has been sidelined in the proposal as requested by the biofuels lobby, which makes me worry that the deforestation impacts of those fuels could go uncounted.”