They also faced two other counts of defaulting to pay Sh434.9 million in the year 2017.
The suspects also defaulted to remit Sh522.9 million in the year 2018.
The suspects pleaded not guilty and were released on a bond of Sh20 million and a surety of the same amount.
Two businessmen were on Friday charged before Mombasa Chief Magistrate Edna Nyaloti with evading tax worth Sh1.5 billion.
The traders, Rahim Qasim and Rameez Gulzar Ali alongside their firm Jhulay Lal Commodities limited were found to have been importing rice into the country while deliberately failing to pay Income Tax.