As far as I understand normally headquarters would mean the station where the government servant is posted. It may imply the city or town where he is posted. However, in cases where an officer is in charge of a particular area which is larger than a town, etc., such as a district, then he may not need permission to visit anywhere in his area. For example, Superintendent of Police is posted as in charge of a district; therefore, he would not need permission to visit anywhere within his district; but, if he goes outside his district, he may need permission to go out of the his area.
In other cases, as mentioned above, in my opinion, the headquarters should mean the station or town where such government servant is posted or employed.
In may opinion, it may not be correct to say that headquarters would mean the place where the records about the employee are kept. It should be the place where the employee is posted.
However, if your department is giving you some other interpretation, then you have to seek clarification from the department itself if there is some confusion about its interpretation. If needed, you may request the department to quote the relevant rules / orders to support the view that it is taking.
Dr. Ashok Dhamija is a New Delhi based Supreme Court Advocate and author of law books. Read more about him by clicking here. List of his Forum Replies. List of his other articles. List of his Quora Answers. List of his YouTube Videos.