In its 19-page submission, the agency said the Centre's proposals were "contradiction to give functional autonomy" and "violative of very principles of natural justice."
The government in its proposal has rejected "pre-condition" of taking views of outgoing CBI Director in the appointment of its new chief.
It has also not agreed to increase the tenure of the Director from two years to three years.
The Centre in its affidavit dated August 2 had also refused to agree to CBI's demand to give its Director status of ex-officio Secretary to the Government of India saying issues of parity had to be kept in mind.
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According to the agency, "Taking views of outgoing Director in appointing a new Director is a statutory provision in existence (CVC Act, 2003). GoI wishes to take it away while terming it as precondition that is not acceptable whereas GoI agrees to incorporate the same by an executive order."
On the issue of tenure of the Director and process of removal, the agency is of the view that, "GoI does not preclude a longer term but does not intend to increase it by legislation. This view is in contradiction to give functional autonomy to the CBI.