The direction was given by the division bench headed by Justice P V Hardas on a petition filed by activist Ketan Tirodkar which alleges that a government panel's report had indicted the company for substandard engines in Chevrolet Tavera BS3 (2.5L variant) and BS4 (2.0L variant).
The reply is to be filed by November end.
According to the PIL, in July 2013 GM recalled 1.14 lakh units of its multi-purpose vehicle to address emission and specification issues.
The PIL alleges that though the government panel indicted the company, no case was filed against GM because the panel was not vested with express jurisdiction to register an FIR.
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However CBI has filed an affidavit saying it would not be able to take up the case as it is overburdened, and also because the case does not have inter-state ramifications as GM has plants only in Gujarat and Maharashtra.
The central agency has also said in its affidavit that "the alleged offence would not attract cheating clause as attributed by the petitioner, but can be treated only as an offence civil in nature".
The petitioner can also file a case under the Consumer Protection Act, it says.