His appointment, cleared by a Cabinet panel, came at a time when the Department will be monitoring payment of taxes by declarants of black money through a four-month long window.
The appointment was officially announced through a press note by the Department of Personnel. Nair retires this month-end.
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Chandra, a 1980 batch officer of Indian Revenue Service (Income Tax cadre), is currently Member (Investigation) of the CBDT.
IIT graduate Chandra's tenure will last till May next year, official sources said.
Nair, a 1979 batch IRS officer, had taken over as CBDT chief on August 1 this year.
The CBDT is headed by a chairman and can have a maximum of six members.