The case has echoes of one against Volkswagen, which pleaded guilty to criminal conspiracy as part of a widespread emissions-cheating scheme. In both cases, the government focused on software in vehicles that can adjust emissions levels.

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The Environmental Protection Agency on Thursday accused Fiat Chrysler of installing secret software that allowed more than 100,000 of its diesel vehicles to emit pollutants above legal levels.

The case has echoes of one against Volkswagen, which on Wednesday pleaded guilty to criminal conspiracy as part of a widespread emissions-cheating scheme. In both cases, the government focused on software in vehicles that can adjust emissions levels.

The accusations against Fiat Chrysler also appeared to be part of a last push by the Obama administration to finish investigations and negotiations involving companies.

The emissions breach described by the government “threatens public health by polluting the air we breathe,” said Cynthia Giles, an assistant administrator at the EPA. She said the software in question resulted in excess emissions of nitrogen oxides, which have harmful health effects.

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Giles stopped short of describing the software as a defeat device of the sort used by Volkswagen to cheat on diesel-emissions tests. But she said there was no doubt that Fiat Chrysler’s software “is contributing to illegal pollution.”

Sergio Marchionne, chief executive of Fiat Chrysler, mounted an impassioned defense, denying it had intentionally broken the law.

“There’s not a guy” at the automaker “who would try something as stupid” as cheating on emissions tests, he said on a call with reporters.

“We don’t belong to a class of criminals,” Marchionne said. “We have done, in our view, nothing that is illegal.”

The 104,000 affected vehicles include the light-duty model year 2014, 2015 and 2016 Jeep Grand Cherokees and Dodge Ram 1500 trucks with 3-liter diesel engines sold in the United States, the EPA said.

At issue is software installed in all modern diesel vehicles that calibrates an engine’s performance and controls emissions levels. Federal regulations allow diesel cars to shut off emissions controls in certain situations — to protect an engine from overheating, for example.

In the Volkswagen case, illegal software caused cars to shut down emissions controls completely during normal driving conditions. In the case involving Fiat Chrysler, emissions controls in the affected cars shut down only during some driving conditions, according to the EPA.

Still, the agency thinks that the software in the Fiat Chrysler cars caused emissions controls to shut down in too many situations — including normal driving conditions.

Marchionne rejected the accusations. Fiat Chrysler’s emissions-control systems met legal requirements, he said.

The company said it had spent months responding to questions from federal regulators and had proposed remedies to address their concerns, including extensive software changes to emissions-control systems that the automaker said could be made immediately.

John German, senior fellow at the International Council on Clean Transportation, whose initial work on Volkswagen’s emissions levels exposed cheating at the automaker, said the EPA’s case against Fiat Chrysler was not as clear-cut. Nonetheless, he said he expected Fiat Chrysler to have difficulty defending itself.

The complexity of modern diesel technology, and the trade-off between emissions controls and engine performance, had motivated automakers like Fiat Chrysler to cut corners, he said.

“It’s very enticing to take shortcuts,” he said. “But it’s absolutely possible for a diesel car to fully comply with U.S. emissions standards, and have good drivability and performance,” he said. “It just costs money.”

If Fiat Chrysler is found to have violated the Clean Act Act, as the EPA says, it faces potential penalties of up to $44,500 for each affected car, or more than $4.5 billion in total.