Baig was sentenced to death for his involvement in the German bakery blast after Maharashtra ATS filed a charge sheet against him claiming he had accompanied Indian Mujahideen co-founder Yasin Bhatkal to carry out the terror attack.
However, neither Delhi Police nor Bangalore Police mentions the presence of Baig in German Bakery blast.
Shinde told reporters here today that "at this stage, nothing can be done. It is preliminary investigation. Unless the whole investigation is done, at this stage we cannot come to any conclusion".
Shinde, however, ruled out ordering a probe to find out the truth over the conflicting views of state police forces.
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Siddiqui was killed in a prison in Pune in June 2012.
The Home Minister indicated if Baig is found innocent, no action will be taken against him.
The NIA had come to the conclusion that the Malegaon blast was the handiwork of right wing radical groups.
He had said at that time that the interrogation was done by Maharashtra ATS and now with the arrest of Yasin Bhatkal, further investigation will be done and more interrogation will be carried out which will bring to light more facts.