The Securities Appellate Tribunal (SAT), by a majority order, gave Financial Technologies India limited (FTIL) four weeks to divest its shares in bourses, including MCX-SX.
"An order passed by one regulator would have to de-facto apply to other regulators and not following this principle would defeat the spirit of regulation," Presiding Officer J P Devdhar said.
He said the moot question was if the orders of one regulator have a bearing on others, and ruled in favour of Sebi, saying the trades regulated by the commodity markets regulator Forward Markets Commission (FMC) are similar to those taken care of by Sebi.
Sebi's order had followed a similar directive by the FMC after a Rs 5,600-crore payment scam in NSEL came to light. FTIL owned 99.99 per cent of NSEL.
SAT member A S Lamba gave a contrarian view and termed Sebi order as "unprofessional".
Devadhar said that as the 90-day window granted to FTIL by SEBI for divesting its stakes had already expired, the company can take another four weeks to exit its holdings.
FTIL owns 26 per cent in commodities bourse MCX and has a 70 per cent stake in MCX-SX and MCX-SX Clearing Corporation. Its MCX-SX ownership is at 5 per cent through equity and the rest through convertible warrants.
At the time of the Sebi order, FTIL and MCX held just under 5 per cent stake in the stock exchange MCX-SX.
FTIL and MCX had 4.99 per cent stake each in the stock exchange as on March, 2014.
The troubled company also has stakes in the Delhi Stock Exchange and Vadodara Stock Exchange in addition to a small holding in the NSE.
The Securities and Exchange Board of India (Sebi) had passed an order on March 19 stating that FTIL was not "fit and proper" to hold any stakes in any of these exchanges.
The Sebi order followed a similar one on December 17, 2013, by commodities watchdog FMC against the company and its promoter Jignesh Shah and key officials like Joseph Massey.