*(that is, "The Ministry of Land, Infrastructure, Transport and Tourism")
Let's take a look how:
Until now, tolls on the superhighway system have been calculated by distance traveled, and there has been a fairly long list of targeted discounts that drivers can use to reduce their toll. The most widely known discount is the 休日上限, which caps a single trip's toll at 1000 yen on weekends and national holidays. But, other discounts, such as commuter discounts (50% off distances under 100 km during commuting hours on weekdays) and late night/early morning discounts (50% off all travel commenced or finished between 10 p.m. and 6 a.m.), have also been automatically applied to relevant tolls. Until now, these discounts have only applied to ETC system users.
From April, 2011, however, this system will change dramatically for individual drivers. The 休日上限 will remain, capping all weekend and holiday travel at 1000 yen. In place of all other discounts, however, a new weekday discount (平日割引) will be used, which caps all travel during a weekday depending on the size of your vehicle. Normal "white plate" cars will be capped at 2000 yen per use of the highway. Smaller "yellow plate" cars and cars designated as eco cars, such as hybrids and electric vehicles, will be capped at 1000 yen per use of the highway. Furthermore, these weekday discounts will apply to all cars, regardless of whether they are using ETC or paying with cash.
The weekend discount, however, will continue to apply only to cars equipped with an ETC reader, and herein lies the loophole that continues to make ETC worthwhile to own: Cars who travel on weekends and pay in cash are still subject to the entire regular toll based on the distance they traveled without any caps or discounts.
So, that covers the bulk of it. There are some further details regarding specific superhighway lines and toll roads which are not part of the 高速道路 network. (For example, use of the Tokyo Aqua Line, a bridge-tunnel between central Tokyo and rural Chiba, is subject to its own fare system.) To check out all the other details, check out this Car Watch link (Japanese) for a simple run down or this exhaustive, mind-boggling PDF press release from the Ministry of blah, blah, Transport and blah (also Japanese) for complete explanations of all changes across the country and rationalization for said changes.
(By the way, former discount systems, such as the commuter discount and late night/early morning discount, will continue to exist and apply to commercial drivers. So, if you are a professional driver in Japan, pretty much nothing changes for you in April.)