Is that they too run a relatively large trade surplus against the US
Based on 2017 trade, the US only has a bigger trade deficit against China and Mexico than it does with Japan.
And that gives Japanese authorities more reasons to worry if China is being harassed heavily to reduce their trade surplus with the US.
Should China exports be more expensive in the US because of the tariffs implemented, it means that US businesses will have to source their goods elsewhere and indirectly it would make Japan's trade surplus with the US even larger than it already is now.
If that were to happen, it surely won't make Trump too happy as he seeks to lower the US' bilateral trade balances with its allies.
Japan has previously said that they aren't looking into bilateral talks with the US, so if that's out of the window then it only makes sense that they don't go about things like the way China are doing right now.
Sometimes, silence is golden.
"I heard that you're running a trade surplus with us too".