The tribunal has also directed the state government to file an FIR against Choudhary for provoking the doctors to strike.
The tribunal has directed the cost to be recovered from the salary of Choudhary drawn in the past six months.
The bench of members Shravan Sahni and Bannalal has also directed Choudhary to join the duty as per transfer orders by December 29.
The tribunal, while observing that 300 patients have reportedly died during the strike by doctors, has also given directions to file FIRs against the doctors responsible for these deaths.
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Government counsel Mukul Singhvi said that his transfer was a routine administrative procedure and there was no ill- will.
"Choudhary has served on his previous post for five years and his case was due for transfer. There was no ill-will on the part of the state government in order of transfer of Choudhary...," Singhvi argued.
Before this, Choudhary's plea to seek an interim protection apprehending any action against him, the high court had also rejected his petition stating it inappropriate to pass any direction with the petition pending before the appellate tribunal.
The tribunal order came a day after the high court gave directions to the state government to take action against the agitating doctors if they do not resume work.
Agitating Rajasthan government doctors met a group of ministers today as part to attempts to resolve an 11-day deadlock over their demands related better work conditions including salary benefits.
The meeting was scheduled following Rajasthan High Court directives for action against the doctors who do not resume work by December 26.