There is no general registration requirement for commercial contracts. Material contracts of publicly-traded companies may require limited disclosure.
Patent license or trademark license for statutory exclusivity requires registration to be enforceable. Registration of non-exclusive licenses for trademarks is possible in order to put potential buyers of the trademarks on notice of the license. Such registration is, however, not required.
Registration of copyright licenses is not available in Japan, although transfer or assignment of copyrights can be registered to assert such assigned rights against third parties.