Mysql [Warning] Using a password on the command line interface can be insecure.

If your MySQL client/server version is a 5.6.x a way to avoid the WARNING message are using the mysql_config_editor tools:

mysql_config_editor set --login-path=local --host=localhost --user=username --password

Then you can use in your shell script:

mysql --login-path=local  -e "statement"

Instead of:

mysql -u username -p pass -e "statement"