The US Department of Justice said it marked the largest civil penalty ever secured under the four-decade-old Clean Air Act.
"This will send a strong message that cheating is not profitable, and that any company that violates the law will be held to account" said Attorney General Eric Holder.
The settlement involved the sale of nearly 1.2 million vehicles, many of which now need to reduce their stated fuel economy by one to two miles per gallon.
The result is that the six vehicle models implicated will emit approximately 4.75 million metric tons of greenhouse gases, above and beyond what the automakers certified with the Environmental Protection Agency.
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As part of the settlement, Hyundai and Kia will "forfeit the greenhouse gas credits that the companies wrongly claimed based on their inaccurate reporting," Holder said.
The automakers also agreed to have an independent certification test group oversee its fuel economy testing, training, data management and reporting in the future.
"Businesses that play by the rules shouldn't have to compete with those breaking the law," said EPA Administrator Gina McCarthy, describing the settlement as "historic."
"This settlement upholds the integrity of the nation's fuel economy and greenhouse gas programs and supports all Americans who want to save fuel costs and reduce their environmental impact."
Hyundai said in a statement that the agreement requires the company to adjust about a quarter of its 2011-13 model year vehicles, reducing their combined city/highway fuel economy by one to two miles per gallon.
"Hyundai has acted transparently, reimbursed affected customers and fully cooperated with the EPA throughout the course of its investigation," said David Zuchowski, president and CEO of Hyundai Motor America.