Programmatic freedom of faculty and researchers is fundamental to creation of knowledge, as everything has to be open to question and scepticism. The universities and academic institutions are established as autonomous institutions to ensure academic freedom. However, it is observed that the autonomy of academic institutions tends to result in centralisation of power in the hands of institutional heads, and is misappropriated to curtail programmatic autonomy of individual academics. The recent penal measures taken against some faculty members of the Kerala Agricultural University are analysed against this backdrop.