The report is the latest episode in a growing list of data falsifications in Japan that has tarnished the image of the country's manufacturing industry, known for high-quality, efficient production.
Representatives for Mazda and Suzuki confirmed they submitted reports regarding improper testing to the ministry but declined further comment. Yamaha Motor confirmed it carried out inappropriate testing.
"Regarding the emissions inspections... it is a fact that there were improper actions," a Yamaha spokesman said. "We sincerely apologize."
Mazda shares were down as much as 1.8 percent, their lowest in nearly 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. Yamaha shares were down 4 percent.
In July this year, Nissan admitted it had improperly measured exhaust emissions and fuel economy for 19 vehicle models sold in Japan.
Many of the automakers, already hit by lacklustre sales, have also been under pressure from U.S. President Donald Trump's proposed tariffs on imported vehicles.