The resignation came hours ahead of a scheduled board meeting of MCX-SX, where former LIC Chairman Thomas Mathew T has taken over as new Chairman.
Sebi is looking at ways to assuage the concerns of investors, trading members and other stakeholders in MCX-SX, according to senior officials.
Meanwhile, Finance Minister P Chidambaram said he hopes that directors of MCX-SX would act in public interest and that there was an orderly resolution of the crisis.
Surprisingly, the PE has also been registered against Sebi's former chairman C B Bhave and ex-member K M Abraham, besides MCX-SX promoters FTIL and MCX. Bhave and Abraham were said to have been opposed to the grant of licence until the exchange met strict guidelines set out by the regulator.
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Pillai said MCX-SX is run by a professional management team and has an eminent board.
"We have also been successful in rationalising costs in a significant manner, which will improve our balance sheet in times to come. It was a wonderful experience to work with the team and I am stepping down due to personal reasons," he added.