Special public prosecutor Deepak Salvi confirmed the development but refused to divulge details.
The special judge G A Sanap directed CBI, which investigated the blasts, to file its reply.
CBI sources said the application does not cite specific ground and appears to be an attempt to delay the trial.
Thirteen powerful blasts that rocked Mumbai on March 12, 1993 killed 257 persons while injuring 713.
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