Is it worth filing patent term extension in Japan when expected patent term extension is only a few weeks or even a few days?

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Yes, in Japan there is a “de facto” exclusivity that in effect extends your exclusivity even after the patent expiration.

Japan has unique Price Listing System to control price of drugs. Patients can receive benefit from National Health Insurance (NHI) only for drugs that are listed in so called NHI price listing. Therefore, in most cases, generic companies cannot practically (not legally) market their generic drugs even after they obtain approvals as generic drugs until and unless they further obtain NHI price listing. Even more, in current practice, NHI price listing for generic drugs can be done only twice a year.

For generic drugs, generic drugs approved by a reference date in February (which is announced every year, but is likely to be around 15th of February) will be listed in June and drugs approved by a reference date in August  (which is announced every year, but is likely to be around 15th of August) will be listed in December (fiscal year 2012). Under this system, if your original patent expires on February 14th, without patent term extension, generics are likely to enter the market in June. However, if you extend your patent only by two days until February 16th, generics are unlikely to enter the market in December. In this scenario, two day patent term extension virtually gives about 10 months extra “de facto” exclusivity.

Thus, it is often recommend to file a patent term extension even if it (legally) gives a patent term extension only by a few weeks or even a few days.