Deduct salary for late attendance in a semi autonomous govt insti

Senior Scientist with 5 yr service period at a semi autonomous institute at pay band PB-4, returned from developed country with competitive fellowship from Govt of India. Several Honors of international quality. Highly productive with several publication in scientific journals of international repute within 5 yrs service-- by any international standard. Sudden change in Director at the institute. Gauge of assessment altered (which is against scientific ethos) by office order to monitor exact number of hours to be calculated within institute by an act of swiping in, swiping out digital access card. Office order reads automated salary will be cut if total period spent inside institute less than what required. Scientists work 24/7 and need to be assessed by their contribution to international standing, publication and over all scientific output— not by cliche as applicable for other regular employees. Not being at premises usually imply exploring scientific collaboration, describing results in form of manuscript that requires unperturbed environment. Scientists at this level need to be trusted, regarded for freedom— else its humiliating and may lead to simple attrition and may be relocating back. Scientists need to be strictly regulated based on their over all scientific productivity than micro managing, which has proven to be no utility for several scientists with perfect record of attendance who are seldom productive scientifically but impeccable office record as they work 9-5pm! Question: how legal it is for the institute to deduct salary based on the office order for govt servants at a grant-in-aid scientific research institute, setting aside the numerous unrecorded late working hours, which is no secret at the institute. Would my appeal against salary cut hold any water in a court of law as this is against scientific temperament and unproductive ruling?