As you'd expect, given the local custom of driving in the left hand lane, the vast majority of vehicles on Japanese roads are right hand drive. Despite local driving tradition, it is perfectly legal to drive a left hand drive vehicle on Japanese roads, provided of course you stay in the left hand lane, and therein lies the danger to cyclists.
Being the driver of a right hand vehicle on occasion, I'm acutely aware of my position in relation to the oncoming traffic as its on my right hand side, closest to me. As a result I position the car close, but not too close, to the center line of the road. I do this because I'm am less aware of the position of the left hand side of my car, and don't want to accidentally hit a parked car, opening door, or heaven forbid a fellow cyclist. When I overtake a cyclist I tend to overcompensate and give them plenty of room, again because I'm less aware of the position of the left side of my car than the right. Best to err on the side of caution.
You might imagine that because the driver of a left hand drive vehicle is sitting on the sidewalk side of their car that they would be more aware of cyclists and thus give us all a little more space when overtaking, but the exact opposite is true. I believe that there are two possible reasons for this. My first theory is that because they are less aware of how close the right hand side of their car is to the center line, and thus oncoming traffic, that they overcompensate by driving closer to the sidewalk more attentive to oncoming traffic than cyclists with whom they share a lane. My second theory is that because they're on the cyclist side of the vehicle that they're well aware of our relative positions and don't need to overcompensate as much as the driver of a right hand drive vehicle and thus overtake more closely.
Of the two I'm hoping that my second theory is the accurate one, but whichever it is, it still boils down to the fact that drivers of left hand vehicles will regularly overtake you way too close for comfort.
Having said this, in general space tolerances in Japan are a lot finer than in other countries. Cars parked within a centimeter of a wall, drivers folding in their side mirrors to allow an oncoming car to pass by, sidewalk cyclists passing within a whisker of pedestrians, being pressed bodily against someone on a train, its common place, and the fact that these fine tolerances translate to the roads keeps us cyclists on our toes.