If you're really concerned about this, then you need to wear something that will filter both particulates and organics. So - perhaps a RESPRO (http://www.respro.com/). Japanese vehicles - especially heavy ones, have crap for emission standards and controls - thus you are inhaling literally tons of dispearsed particulates and organics. If you want something to start - then just about ANY multi-layer particulate mask would be a very good start. I often wear one when riding in especially cold or dusty seasons - it really helps. As for commuting - if I had to follow the main motorway paths every day I'd get a Respro. Diesel engine particulate is highly carcinogenic. And if you can cut down on the organics - that's even better.
Particulates are the soot byproducts, stirred up dust, micro-particles and anything else that is in suspension in the air and when you breathe it - it becomes lodged in your sensitive lung tissue, sometimes to linger there for years festering all sorts of nasty issues from lesions and chronic inflammation to cancer.
Organics are the solvents and vapours that are common combustion and industrial byproducts. Stuff like Sulpher Dioxide, Benzenes, heavy hydrocarbons, Ozone, etc. They are often in very high concentration close to motorways and factories.
Any activity that increases your respiration will also increase your intake of these. The more your breathe, the more damage it does. So, any reduction is good. As I said, Diesel particulate is really nasty - and not well managed in Japan. A multi-layer mask like the kind you get at conbinis will cut alot of this out of the air you breathe. In order to cut out the organics you need a more sophisticated, sealed filter system.
BTW - In my former life I was a California Licensed SMOG Inspector and Instructor. Air quality in California is a very very serious matter. The EPA and SCAQMB is feared more than the IRS.