One of the major considerations on the supply side is that many of Japan's refineries are in the affected Tohoku region, and are currently shut down. Based on the map they were showing, they've got about 2 refinaries running, down from somewhere in the 11-15 range. The 2 running are located in central and western Japan, so there is additional distance that supplies have to be hauled.
The problems with transport are the ones one would expect after a major earthquake: massive infrastructure damage. Typically fuel would be shipped in via the sea then put onto tankers and distributed inland from there. However, the ports in the region were severely affected, so this is not an option at the moment. Fuel must come in from shipments via the Sea of Japan side of the country and be tanked in from there. This increases the amount of time ships take to get to the appropriate port. In addition, there is still damage to roads that must be repaired for the tankers to get through. One factor they didn't mention but must have contributed for the past couple of days is that the area just had a snowstorm blow through that would slow any trucks trying to make their way through damaged areas.
Things do improve day by day as rescue and cleanup efforts progress. It's just a matter of time working through the difficulties in the meantime.