This can be due to 2 main issues. The problem is one might be staying too far to go to LCCT.

1) They may need explanation on the item.
2) Need to pay tax

Most likely it is reason #1 because for #2, your agent can clear the tax. You just need to wire the money.

Since electricity in Japan is different from Malaysia, they might want you to get SIRIM QAS. If the product is being sold in Malaysia, then this might not be problem because someone has submit for approval before. However, if this is something new, then they may require you to submit the sample to SIRIM for testing. I think electrical/electronic product is not a problem because the product sure has met standard like UL and also CE. SIRIM might not need to do testing at all.

Maybe custom need owner to be there so that you can open the box contents in front of them to explain everything. All these exercise usually random and probably not your lucky day.

The agent need to be knowledgeable to give proper explanation to custom or SIRIM. If not, a problem like this will happen.