“That is an astronomically high level of smog-forming pollution,” he added. “It’s happening at ground level where people are breathing the fumes. And if the problem extends to other vehicles it’s almost unimaginable what the health impact will be.”

The E.P.A.’s Office of Civil Enforcement, which is largely staffed with career civil servants, has been conducting the investigation into diesel tuners for about five years, since it discovered the cheating by Volkswagen. An E.P.A. official familiar with the report, who spoke on condition of anonymity because he was not authorized to speak on the record, said it represents a significant milestone in the ongoing investigation.

The report was completed last week, though the E.P.A. has not publicized it or issued a news release, which stands in contrast to the media blitz assembled by the Obama-era agency for the Volkswagen investigation. In this instance, word got out after Evan Belser, the deputy director of the office’s Air Enforcement Division, emailed a copy of the report to the heads of three state air pollution control organizations.

A spokesman for the E.P.A., James Hewitt, initially said Wednesday that he was unfamiliar with the report. In a statement emailed after he was informed of it, Mr. Hewitt said, “Under our National Compliance Initiative, in FY 2020, E.P.A., resolved more civil tampering and aftermarket defeat device cases (31) that prevented more motor vehicle emissions (14.6 million pounds) than in any prior year in the agency’s history. Additionally, E.P.A. has assessed more in civil penalties, criminal fines, and restitution under this administration than the first four years of the Obama administration.”

The report studied only diesel pickup trucks weighing between 8,500 pounds and 14,000 pounds, but E.P.A. analysts believe the cheating has spread across American garages and highways.

“One reason it is difficult to estimate the full extent of tampering nationwide is that the Air Enforcement Division has reason to believe this conduct occurs within most or all categories of vehicles and engines, including commercial trucks, passenger vehicles, pickup trucks, motorcycles, forestry equipment and agricultural equipment,” the report concluded.

“The aftermarket defeat device problem is huge,” said Phillip Brooks, a former E.P.A. emissions investigator who worked on the diesel tuner investigation and the Volkswagen case. “A lot of people just don’t understand what the problem is — your average person buys a vehicle and says, it’s my vehicle, I can do what I want with it. They may not even be aware that these devices are illegal.”

“But,” he continued, “the real question is impact. If 10 people do it, there’s no impact. But these are numbers that are meaningful for air quality.”

“This is not a great way to express how to be a free American, but there are a lot of people out there who think that way,” Mr. Brooks concluded.

Retailers generally sell the illegal defeat devices online and in public, the report said, but “operate in a secretive manner such that the nature and extent of their operations are not reflected in their business records.”

The E.P.A. investigators found at least 28 different companies involved with the manufacturing of at least 45 diesel tuners. The report does not name the companies because, it says, E.P.A.’s investigation of the matter is ongoing.

A crackdown on the diesel-tuner market would be far more difficult than pursuing a single company like Volkswagen. “There’s a lot of small businesses in play; it’s more difficult to enforce than the one big global automaker,” said Mr. Kodjak of the International Council on Clean Transportation. “Amazon sells diesel tuning equipment. You can retune your engine for $400.”

“Not all of these are illegal, by any means,” he added. “A lot of them are mom-and-pop places.”

Over the course of its investigation, the E.P.A. has shut down some manufacturers: Earlier this year, the agency reached an $850,000 settlement with Punch It Performance and Tuning, a small Florida company that had been selling illegal diesel tuners online.

According to E.P.A. documents, the settlement was lower “due to their limited financial ability to pay a higher penalty. In order to pay this penalty, Defendants have represented that they will sell residential real estate properties that they purchased with profits made from the manufacture and sale of defeat devices.”

Experts said the findings also point to weaknesses in state and local emissions inspection programs, which are entrusted to make sure cars and trucks comply with environmental law and emissions standards.

Federal funding for state enforcement programs has been flat for more than a decade. The E.P.A.’s budget for state and local implementation of the Clean Air Act has been the same every year since 2004: $228 million.

“There are state and local codes and laws in place to crack down on this,” said Miles Keough, the executive director of the National Association of Clean Air Agencies. “But they are all running on the same small budget.”

At many state and municipal emissions inspections stations, inspectors do not actually test tailpipe emissions, explained Mr. Brooks. Instead, they use computers simply to get readings from a vehicle’s computer.

With a defeat device, he said, “the computer on the truck tells the computer at the emissions station, everything’s fine.”