Suzuki Motor on Wednesday apologized for using testing methods that do not comply with government regulations, but it said there was no falsification of data.
"I deeply apologize for not having gathered data in accordance with Japan's regulations," company chairman Osamu Suzuki told a news conference.
But Suzuki said no changes were needed to the fuel economy data of the affected vehicles as differences in test results were within the margin of error.
The carmaker denied that the non-compliance was intended to boost the reported fuel economy of its vehicles.
No vehicles sold under the Suzuki brand overseas had been affected, the carmaker said.
The announcement came after rival Mitsubishi Motors acknowledged last month it had persisted in using outdating fuel economy tests since new regulations were introduced in 1991.
The scandal at Mitsubishi prompted the Transport Ministry to urge all Japanese carmakers to check by Wednesday for similar issues.
Suzuki has not manipulated fuel economy data in the same way as Mitsubishi, Kyodo News agency reported earlier, citing unnamed sources at the company.
Shares in Suzuki closed down 9.37 per cent after falling as much as 15 per cent.