The EPA has issued a notice of violation against Fiat Chrysler and launched investigations into the car manufacturer's Jeep Cherokee and Dodge Ram vehicles.
The undisclosed software results in increased emissions of nitrous oxides from the vehicles and the allegations cover roughly 104,000 vehicles.
Allegations could reignite the emissions scandal that rocked the automotive sector when it was revealed Volkswagen had installed software that masked the amount of emissions its diesel cars produced.
Cynthia Giles, assistant administrator for the EPA’s office of enforcement and compliance assurance, said: "Failing to disclose software that affects emissions in a vehicle’s engine is a serious violation of the law, which can result in harmful pollution in the air we breathe.
"We continue to investigate the nature and impact of these devices. All automakers must play by the same rules, and we will continue to hold companies accountable that gain an unfair and illegal competitive advantage."
The Clean Air Act in the US requires vehicle manufacturers to disclose and explain any software, known as auxiliary emission control devices, that can alter how a vehicle emits air pollution.
However, Fiat Chrysler is being accused of not disclosing the existence of certain auxiliary emission control devices despite being aware that such a disclosure was mandatory.
The EPA is also investigating whether the auxiliary emission control devices constitute "defeat devices," which are illegal.
Mary D. Nichols, chair of the California Air Resources Board, added: "Once again, a major automaker made the business decision to skirt the rules and got caught.
"Carb and US EPA made a commitment to enhanced testing as the Volkswagen case developed, and this is a result of that collaboration."