Uttrakhand's Chief Secretary S Ramaswamy said that Parag Madhukar Dhakate has been replaced by Dheeraj Pandey as Director.
D V S Khati, the Chief Wildlife Warden, said that Dhakate was not authorised to issue any such order.
Last week, Dhakate had issued shoot-at-sight order and pressed two drones into service after movement of poachers was reported along the southern fringes of the park.
150 forest officials were deployed and a total of 388 camera traps installed at sensitive points within the territory of the park.
The order, however, raised eyebrows following which Dhakate has been removed from his post.