The US Environmental Protection Agency has accused a second major car company, Fiat Chrysler, of cheating on its diesel emissions testing by using secret software applications in multiple models.

The company’s Jeep Cherokee and Dodge Ram vehicles used “management software” that “increases air pollution” from nitrogen oxides for three years, the EPA alleged in a notice of violation issued Thursday.

Fiat Chrysler said it was “disappointed” in the citation, and it “believes” its emission control systems met applicable requirements.

“All automakers must play by the same rules, and we will continue to hold companies accountable that gain an unfair and illegal competitive advantage,” said Cynthia Giles, assistant administrator for EPA’s office of enforcement and compliance assurance.

Volkswagen was accused of using similar software on its own diesel vehicles to mask the emissions of the same greenhouse gas in September 2015. Multiple regulators slapped the automaker with $15bn in fines and consumers the world over filed class-action lawsuits against the firm. Shares of Fiat Chrysler immediately dropped 16% on the news.

Sergio Marchionne, CEO of Fiat Chrysler, objected to comparisons of Volkswagen and Fiat Chrysler, suggesting that conflating the two was evidence of a different kind of unlawful emission: Anyone who compares Fiat to VW “is smoking illegal material,” Marchionne told Reuters. The jibe is a favorite of Marchionne’s, who accused Mormon former presidential candidate Mitt Romney of the same for objecting to the auto industry bailout.

The software used by Fiat Chrysler lowered the emissions of nitrogen oxides during testing, the EPA alleges. “By failing to disclose this software and then selling vehicles that contained it, FCA [Fiat Chrysler Automobiles] violated important provisions of the Clean Air Act.”

The EPA said it had the authority to force Fiat Chrysler to recall the 2014, 2015 and 2016 Cherokee SUVs and Ram pickup trucks – some 104,000 automobiles – but that it had not yet decided to do so. “Any follow-up action, including the need for a recall, will be determined as part of the ongoing investigation,” spokespeople for the regulator wrote. In general, regulators offer manufacturers a chance to voluntarily recall their product before forcing a recall.

Fiat Chrysler “believes that its emission control systems meet the applicable requirements,” the company said in a prepared statement. Fiat Chrysler did not address the EPA’s allegations that the car company had hidden the software from the regulator, instead stating that lowering its cars’ emissions during testing was necessary to “balance EPA’s regulatory requirements for low nitrogen oxide (NOx) emissions and requirements for engine durability and performance, safety and fuel efficiency”.

Michelle Krebs, senior analyst with Autotrader, said: “We need to be careful not to jump to the conclusion that the Fiat Chrysler diesel situation is the same as the Volkswagen one. It is clear that the Volkswagen diesel debacle prompted regulators to more closely scrutinize all diesels and obviously they noticed some issues with Fiat Chrysler.”

The EPA is working in conjunction with the California Air Resources Board (CARB) on its citation of Fiat Chrysler. “Once again, a major automaker made the business decision to skirt the rules and got caught,” said CARB chair Mary D Nichols.

• This article was amended on 13 January 2017 because an earlier version referred to nitrous oxide. This has been corrected to say nitrogen oxides.