A dump wagon adds freshly gathered corn cobs to a pile on a farm near Hurley, S.D. in 2007. (Dirk Lammers/AP)

The Environmental Protection Agency set new 2017 targets for biofuels, part of a troubled and complex program to promote non-corn-based ethanol and biodiesel that has fallen far short of the goals Congress adopted in 2007. Moreover, the byzantine enforcement program, strongly criticized by many oil refiners, could end up on President-elect Donald Trump’s chopping block.

The EPA said Wednesday it would nudge up biofuel mandates, requiring U.S. petroleum refiners to mix an additional 100 million gallons of biomass-based biodiesel and an additional 81 million gallons of cellulosic biofuel into the nation’s motor fuel. Overall, the EPA mandated a total of 4.28 billion gallons of advanced biofuels, a 670 million-gallon increase but less than half the goal set by Congress in 2007. An additional 15 billion gallons of biofuels come from well-established corn-based ethanol producers.

The biggest shortfall has been cellulosic ethanol derived from corn husks, switch grass and other non-corn feedstocks. Congress had aimed to stimulate a new industry and envisioned 5.5 billion gallons of production by next year. On Wednesday, the EPA, charged with implementing the program and adjusting targets as needed, set a mandate of just 311 million gallons for cellulosic biofuel.

Nonetheless, the increase in targets was more than what some industry officials expected. And representatives of the ethanol industry said they were pleased. “EPA sent a signal that it is firmly behind this program,” said Bob Dinneen, president of the Renewable Fuels Association. “They are going to drive production and not be bullied by the oil industry, which wants to go backward.”

Currently the nation uses about 14 billion gallons of ethanol and about 2 billion of biodiesel. Each of the gallons of ethanol produced in the United States gets a renewable identification number that can be detached and bought and sold, in some cases by investment banks or other trading companies. At the end of the day, the blenders generate the 38-digit RINs but refiners are required to turn them in to the EPA — in the system’s jargon, the refiners are the “point of obligation.”

RINs can be traded, giving refiners more flexibility to meet the government’s targets. With prices of RINs lurching from pennies to well over $1 a piece, the market is $10 billion to $15 billion in size. And it can be very volatile because the EPA issues its targets so late in the year that buyers and sellers must speculate on what the mandates will be.

On Wednesday, the price of RINs rose 15 to 17 cents a gallon, according to Citigroup, which in a note to investors called the system “RINsanity” and said that the EPA goal was “practically unachievable given the current infrastructure and demand” for motor fuel.

“The volumes here are not great news from our perspective but also not completely unexpected from this Administration,” Stephen H. Brown, vice president for federal government affairs at refiner Tesoro, said in an email. “The program just continues to get unworkable for everyone in the near future.”

Valero, the nation’s largest oil refiner and a major ethanol producer, issued a statement saying that EPA “missed an important opportunity to fix the implementation of the renewable fuel standard.”

Soon, none of this may matter. Trump has indicated that he might ax the RINs program. After Trump gave an economic campaign speech in September, his campaign posted a list of regulations to eliminate, including the tradable credits. However, even if Trump abolishes the RINs trading program, he might still need to come up with a way to meet the renewable fuel standards set in energy legislation passed in 2005 and 2007. On the campaign trail in Iowa, Trump had said he supported the Renewable Fuels Standard.

One reason Trump highlighted the RINs program is that one of his closest supporters and advisers, billionaire investor Carl Icahn, is chairman and majority owner of a company that owns two small refineries. The refineries are expected to pay more than $200 million in 2016 to buy enough renewable fuel certificates to fulfill their obligations under the government’s volume-based rules, according to a JPMorgan Chase note to investors in July. The purchase of those certificates had become the refineries’ biggest operating cost, the firm said.

Trump’s speech came shortly after Icahn sent him a copy of an open letter to EPA administrator Gina McCarthy sent on Aug. 9 urging her to overhaul the program, which Icahn called “the quintessential example of a rigged market.” He said it “has become ‘the mother of all short squeezes,’ ” where retailers don’t want to blend ethanol or choose to hoard their certificates until the last minute to get a better price.

Icahn said the system was threatening to bankrupt companies like his.

Meanwhile, the board of the American Fuel and Petrochemical Manufacturers, whose 400 members include both small and large refiners, voted by a narrow margin to file court papers demanding the program be changed. Instead of requiring refiners to submit to the government enough RINs to cover the refined gallons produced, EPA should shift that burden to the companies that actually mix the ethanol with the gasoline, the group said. Because ethanol corrodes pipelines, it cannot be mixed together with gasoline or diesel at refineries, which are therefore in a poor position to implement standards.

But the American Petroleum Institute, a longtime critic of the RIN program, now says there shouldn’t be any effort to alter it short of abolishing it, which is unlikely to happen. Industry sources, who spoke on the condition of anonymity to maintain business relationships, say that over the past five years some of the country’s biggest integrated oil giants have purchased blending facilities, which generate RINs. That has helped them capture hundreds of millions of dollars in profits from the RIN market. Change could hurt them now.