The unnamed defendants have been released on BND 40,000 ($32,000) bail.
They have a month to seek legal counsel before entering a plea.
Some of the charges relate to Abasa Shipping & Trading for allegedly importing "uncustomed goods" from Lawas, Sarawak, on 38 occasions between January and November 2013, the Brunei Times reported.
Ngu Shipping & Trading is facing similar charges for allegedly abetting the entry.
Two