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.
All three have already complied with a request by the Japanese Ministry of Land, Infrastructure, Transport and Tourism (MLIT) to conduct investigations into the matter.
Suzuki, Japan's fourth-largest automaker, said that of 12,819 sample vehicles tested for fuel economy and emissions since June 2012, around 50 percent of them had been inspected improperly.
The admissions are the latest in a string of scandals involving data falsification and testing standard breaches in Japan's key auto sector.
"I deeply apologize and will lead efforts to prevent recurrence", Suzuki Chief Executive Toshihiro Suzuki told a news conference. Suzuki said almost half of its 12,819 new auto inspections involved improper inspections at its three plants. For Yamaha Motor, around 2 percent of 335 units chosen for the sampling inspection had not gone through appropriate testing since January 2016, according to the ministry. Yamaha shares were down 4 percent.
Suzuki, Mazda and Yamaha said they would take preventive steps, such as changing inspection devices so their staff can not rewrite the data.
Results at Japanese affiliates of three foreign automakers - Audi AG, Volkswagen AG and Volvo Cars - were pending, while no irregularities were reported by the remaining 17 companies, the ministry said.
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.
In July, Nissan admitted data on exhaust emissions and fuel economy had been "altered" for some of its vehicles, and a year ago the firm was forced to recall more than a million vehicles after admitting staff without proper authorisation had carried out some inspections.