Justice P R Ramachandra Menon refused to interfere in execution of the government order.
Natarajan had contended that his suspension was "illegal" and "politically motivated."
The government had suspended Natarajan in November last year following a police probe which came across evidence to corroborate the charge that the commissioner had urged a police official investigating the land gift case to spare Achutanandan.
The case related to alleged irregularities in assigning land to one of the relatives of Achuthanandan when he was the Chief Minister.
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