Agarkar, who grabbed 288 ODI wickets in 191 matches, replaces former cricketer Milind Rege at the helm of affairs of the selection committee for the senior team.
Agarkar, now 39, played his last Test match versus Pakistan in 2006 and last ODI against England in 2007.
The committee headed by Agarkar comprises former India players Nilesh Kulkarni and Jatin Paranjpe and Sunil More, a media release by MCA said.
MCA sources said a decision to this effect was taken by its Cricket Improvement Committee.
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For the Under-16 boys team, Atul Ranade has been appointed as the chairman of the selection committee, which consists of Mandar Phadke, Piyush Soneji and Mayur Kadrekar.
For the Under-14, the selection committee will be headed by Omkar Khavilkar with Sanjeev Jadhav, Nilesh Patwardhan and Mangesh Darekar as members.
Similarly, the MCA also announced committees to chose senior women and girls Under-19 team.
All the committees were selected for 2017-18.