Officials were looking for documents which would support the company's previous claims that it had not meant to deceive car buyers.
Last month Suzuki said it found "discrepancies" in its fuel emissions testing, but denied it was cheating.
Suzuki added the issue did not apply to products sold outside of Japan.
The company issued a statement earlier this week, and clarified that it failed to use testing methods that would comply with Japanese regulations due a lack of manpower, and also a failure on its part to invest in the necessary infrastructure.
Suzuki's shares were down by almost 1% on the Tokyo stock exchange on Friday.
Suzuki is the fourth-largest car company in Japan, after Toyota, Nissan and Honda.
Earlier this year, Japan's transport ministry raided the offices of Mitsubishi Motors, after the carmaker admitted to falsifying its fuel economy data.
The scandal led to the president stepping down, and rival Nissan Motor later stepped in to gain a controlling stake in the embattled company.
Last year Volkswagen admitted to cheating emissions tests in the US.
Authorities found the German carmaker was installing a cheating software in its diesel vehicles that could detect when the cars were being tested and would change emission levels accordingly to improve the results.
Japanese authorities have raided the headquarters of Suzuki, as part of an ongoing probe into the carmaker's use of improper fuel economy tests.