The action comes in the wake of the controversial deal in which a private company was allotted scarce S band spectrum by ISRO allegedly in violation of rules.
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Besides Nair, K Bhaskaranarayana, former scientific secretary at ISRO, K R Sridharamurthi, former managing director of Antrix, commercial arm of ISRO, and K N Shankara, former director of the ISRO satellite centre, have been penalised by the department of space, an ISRO official said.
The contract with Devas was signed during the tenure of Nair as the chairman of ISRO.
Nair was also the person behind India's maiden moon mission Chandrayan I.
The government action comes after considering a report of the high--powered committee that went into the Devas deal and that of another panel, which examined the HPC report.
The prime minister had on May 31, last year constituted a five-member high-level team under the chairmanship of former Central Vigilance Commissioner Pratyush Sinha to examine aspects of the agreement between Antrix and Devas.