TOKYO (AP) _ Japan's trains are fast, clean and almost always on time. But many commuters found out this week that their fabled efficiency doesn't necessarily include charging fares that are, well, fair.

Following an announcement by the country's largest railway that it had inadvertently charged thousands of commuters the wrong fares for more than three years, a half-dozen other railways have admitted they also charged the wrong fares.

``As a train operator, we are ashamed. We apologize for causing passengers trouble,'' Mutsutake Otsuka, the president of the JR East train company, said at a press conference earlier this week.

``It's outrageous,'' said Takako Sakai, a 23-year-old graphic artist in Tokyo. ``I'm glad they caught the mistake. But it's too late to get all worked up about now.''

As of Thursday, seven companies including JR East and two major commuter train operators in Tokyo had reported displaying incorrect fares on lists above automatic ticket machines at their train stations.

JR East, Japan's biggest railway operator, inspected all of its 1,704 stations and found 279 had incorrect signboards, according to a spokesman.

Some passengers traveling on JR East were overcharged anywhere from 20 cents to $4 each time they traveled, while others were undercharged 20 cents to $6.20, according to the company.

JR East says it does not know how much extra money all the commuters paid, but has announced it will pay refunds to anyone who can prove they were overcharged. So far, only 12 refunds have been claimed, totaling $1,545.

Officials at the Transportation Ministry said many of the mistakes were probably made when the train companies raised fares in 1997.

There are about 180 train companies nationwide. The Transportation Ministry said some companies, especially the small and middle-sized ones, are still checking their fares and the number of companies with wrong displays could go up.

``Our ultimate aim is to prevent this from occurring again,'' ministry official Takeshi Hagiwara said.