The officials searched Mitsubishi’s plant in Okazaki.
Mitsubishi has admitted that employees altered data to flatter mileage rates on more than 600,000 vehicles.
A government spokesman said they were treating it as an “extremely serious case” and that it had ordered Mitsubishi to submit a full report.
The authorities have set April 27 as the deadline for Mitsubishi Motors to hand over the report on the inaccurate testing.
Japan’s chief cabinet secretary, Yoshihide Suga, said: “Based on [the findings from] the raid, and a report from the company, we would like to reveal the extent of the inaccuracies as soon as possible.
“We will deal with the situation in a strict manner and would like to make sure of the safety of cars.”
The Okazaki office is Mitsubishi’s second largest plant in Japan and is a manufacturing hub as well as a research facility.
The inaccurate tests involved 157,000 of Mitsubisi’s own cars and 468,000 vehicles produced for Nissan.
The issue affected models including Mitsubishi’s ek Wagon and eK Space, as well as Nissan’s Dayz and Dayz Roox.
All are “mini-cars” with 660cc petrol engines and are popular in Japan but have found little success in other markets.
Shares of Mitsubishi Motors were not traded on April 21 as no buyers could be found to match investors wanting to sell.
Instead, the Tokyo Stock Exchange set an indicated closing price of 583 yen, a 20% drop from yesterday’s close of 733 yen.
Shares in Mitsubishi had already fallen 15% on April 20, when news of the falsified data first emerged.
Mitsubishi had struggled for years to regain consumer trust after a defects scandal in the early 2000s that covered up problems such as failing brakes, faulty clutches and fuel tanks that fell off vehicles.
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