Mr Atwoli yesterday said the sustained attacks against Prof Magoha were being influenced by people who wants the CS out so that they can continue benefiting from multi-million shilling tenders at the ministry.
The Cotu boss appealed to President Uhuru Kenyatta to protect the CS against the cartels.
Addressing a press conference yesterday, Atwoli questioned why the Ethics and Anti-Corruption (EACC) was quick to open investigations into the matter yet many corruption cases were pending.
The trade unionist said instead of EACC probing claims of ghost learners that have continued to cost taxpayers millions of shillings, the agency has resorted to investigating “triviality”.
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Prof Magoha had last week revealed a scandal involving inflation of number of learners in public schools by over 500,000.
Atwoli claimed some individuals were against the CS for allegedly sealing loopholes that have been exploited by cartels in the ministry.
The past few days have seen the CS come under criticism for dressing down a senior ministry official in Uasin Gishu County.
Magoha reportedly gave County Director of Education Gitonga Mbaka a tongue lashing, blaming him for the untidy state of Langas Primary School. The CS later chased him away.
The incident triggered a barrage of accusations against the CS, with Public Service Commission issuing a circular stripping Magoha off powers to carry out human resources functions of the ministry.