In a major blow to the Japanese carmaker, Suzuki Motor announced that the company used improper fuel economy and emissions tests on its vehicles in Japan. The ministry looked at tests conducted over different periods at all three automakers.
The report is the latest episode in a growing list of data falsifications that have tarnished the image of Japan's manufacturing industry, known for its high-quality and efficient production.
All three reported "inappropriate handling" of vehicle inspections, the ministry said.
The company's emissions testing system "was not set up to automatically invalidate results when a speed trace error occurred", it explained, while the level of deviation permitted under the test was at the discretion of each individual inspector. According to a report by the Nikkei Asian Review, Mazda, Suzuki and Yamaha are now caught up in the scandal as well.
They said incomplete emissions tests were done on some of its vehicles, but its officials certified the results as though the tests had been administered properly.
"I deeply apologize and will lead efforts to prevent recurrence", Suzuki Chief Executive Toshihiro Suzuki told a news conference.
Mazda said it 72 vehicles or 3.8 percent of those in its sample were affected, while Yamaha put the figure at 2.1 percent of its motorbike sample. Yamaha shares were down 4 percent.
Both Mazda and Yamaha apologized.
Mazda shares were down as much as 1.8 percent, their lowest in almost four weeks, and Suzuki shares were down as much as 5.2 percent, its worst session since November 2016, versus a 0.5 percent fall in the benchmark Nikkei.
None of the automakers reportedly found problems in their vehicles' correct emissions and fuel economy performance that warranted a recall.
That order was part of a larger inspections scandal that began when Kobe Steel was charged with manipulating data for a wide range of products.
Numerous automakers, already hit by lackluster sales, have also been under pressure from U.S. President Donald Trump's proposed tariffs on imported vehicles.