You have to create a new instance running MySQL 5.6 and move to it. Per this doc on Upgrading MySQL for an Instance <https://cloud.google.com/sql/docs/mysql/upgrade-db>:
The steps for moving your data from one version of MySQL to another involve > exporting data from the current instance and importing that data into the > new instance running the later version of MySQL. > -- You received this message because you are subscribed to the Google Groups "Google App Engine" group. To unsubscribe from this group and stop receiving emails from it, send an email to google-appengine+unsubscr...@googlegroups.com. To post to this group, send email to google-appengine@googlegroups.com. Visit this group at https://groups.google.com/group/google-appengine. To view this discussion on the web visit https://groups.google.com/d/msgid/google-appengine/bed31d4a-e84c-479b-9285-c36084fe1891%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.