You can set idle_in_transaction_session_timeout on the session level in PostgreSQL 9.6 using SET [1]:
SET SESSION idle_in_transaction_session_timeout = '5min';
If you need this to be set at instance level, I recommend opening a Feature Request on the issue tracker website [2] so that the Cloud SQL Team can look into it as this flag is not implemented for Postgres in Cloud SQL [3]
[1] https://www.postgresql.org/docs/current/sql-set.html
[2] https://issuetracker.google.com/
[3] https://cloud.google.com/sql/docs/postgres/flags#list-flags-postgres
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