Control over the permanent is executive is by the political executive i.e. PM and his council of ministers and the Legislature i.e. Parliament.
Legislative control is more theoretical and ineffective even though our constitution has made the legislature supreme our executive and even judiciary as long as it remains within the framework of the constitution:
Executive Control: Control by the political executive over the permanent executive is constant, continuous, stimulative and directive.
Judicial control: All orders, laws, bylaws have to be as per the framework established by the constitution. The laws can be invalidated by judiciary if they are not. This is because judicial review is allowed by the constitution.
Constitution either has "Procedure established by law" which means the judiciary has supreme power over executive and legislature and can declare any act unconstitutional. The Indian constitution has "Due process of law" which means judiciary can declare laws as unconstitutional but the parliament can amend the constitution and override the judiciary.
The state can be sued by citizens for contracts but officials can't. Similarly for wrongful action by officials i.e. torts the state can be sued for non sovereign functions but not sovereign functions. State can't be held liable for actions done by servants in personal capacity.
Limitations: