The Tokyo District Public Prosecutors Office's special investigative unit has already subpoenaed documents from Kobe and suspects the company, Japan's third-largest steelmaker, of criminally misrepresenting data.
"We deeply apologize for causing great trouble to the people involved" and the company will "sincerely respond to the probe and cooperate with the authorities", Kobe Steel said in a statement.
A company spokesman confirmed that the investigation concerned the data tampering but declined to say when the probe had started.
Kobe Steel, which supplies steel parts to manufacturers of cars, planes and trains around the world, has admitted to supplying products with falsified specifications to more than 600 customers, and admitted the data fraud had been going on for almost five decades.
According to the company's final report on the scandal released last month, the steelmaker altered strength and other data to make its products look as if they met specifications sought by clients. Such materials have found their way into automobiles, aircraft and even shinkansen bullet trains.
Company officials will be questioned to determine why the long history of falsified quality data was allowed to continue.
Investigations first revealed that Kobe Steel knowingly shipped at least 20,000 tons of aluminum and copper products with fabricated inspection data.
The scandal-plagued firm also admitted that an internal probe had revealed that 140 tons of iron powder shipped in fiscal 2016 did not meet customer specifications. Affected products have also been used by Central Japan Railway Co.
The scandal has shaken trust in Japanese manufacturing.
The U.S. Justice Department in 2017 ordered Kobe Steel to submit documents related to the data falsification.
In one year alone since 2016, Kobe Steel products were sold to 688 companies in Japan and overseas.
The Kobe Steel spokesman declined to comment on the Nikkei report. A company-commissioned investigation linked five current and former executives to the cheating, which involved more than 40 employees.
Kobe Steel was founded in 1905 and has been a bastion of Japan's manufacturing sector.
Past year saw a slew of scandals related to Japanese manufacturers, including Mitsubishi Materials Corp.'s subsidiaries who were found to have falsified quality data for products used in multiple industries, including in equipment used by Japan's Self-Defense Forces (SDF), which compounded growing concerns about quality control in Japan's manufacturing sector.
Uncertified safety checks were also found to have been routinely carried out by automakers Nissan Motor Co. and Subaru Corp., which led to extensive recalls.