The companies came forward after the ministry last month ordered 23 auto and motorbike companies to conduct in-house probes after it emerged Nissan and Subaru had cheated on fuel economy and emissions data, the latest product quality scandal to hit the country's auto sector.
All three reported "inappropriate handling" of vehicle inspections, the ministry said.
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.
Suzuki admitted improper inspections on 6,401 vehicles, or nearly half of those subject to sample checking, between 2012 and 2018.
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.
The ministry said it would "examine their reports and take strict measures if necessary". It said most of the 20 other companies asked to examine their data had reported no misconduct, while several others were still investigating.
The admissions are the latest in a string of scandals involving data falsification and testing standard breaches in Japan's key auto sector.
In July, Nissan admitted data on exhaust emissions and fuel economy had been "altered" for some of its vehicles, and last year the firm was forced to recall more than a million vehicles after admitting staff without proper authorisation had carried out some inspections.