Assuming the customer is a non- resident of Japan, you should not charge the customer consumption tax on the services. The only exceptions to this rule are:
(a) For transport and storage services for assets located in Japan
(b) For meals and accommodation services provided in Japan
(c) For services available in Japan which are similar to the above (a) and (b)
Services provided to non-residents are regarded as export transactions, and export transactions are tax-exempt.
However if non-residents to whom you have provided the services have a branch or representative office in Japan, the services are not regarded as export transactions. Therefore you should charge the customer consumption tax.