Following the installation of a SharePoint 2013 environment I had an issue where Farm Administration security settings hadn’t been correctly applied. Even though my SharePoint setup user account was listed in the Farm Administrators group and was a local administrator, many options were missing from the Central Administration site. Some of the missing options included manage services on server and I was unable to create new service applications.
In order to correct the permissions, I re-ran the SharePoint 2013 Products Configuration Wizard. When running the wizard I left all the options as they were. Once the wizard had completed the permissions had been set correctly and Central Administration displayed all the options correctly.