The complainant, right to information (RTI) activist Vivek Garg, also sought to call Congress leader Mani Shankar Aiyar and Chandrabhan of the Rajasthan Pradesh Congress as witnesses in the case.
Metropolitan Magistrate Harun Pratap asked Garg to explain why was it relevant to summon the prime minister and Sonia Gandhi as witnesses.
Counsel for the complainant told the court that he wanted these VIPs to be summoned as witnesses as all of them were present in the "Chintan Shivir" of the Congress at Jaipur where Shinde made the alleged remarks.
A complaint was filed seeking registration of an FIR against Shinde for his alleged comments at Jaipur in January.
The court had earlier dismissed the plea for registering the FIR, but allowed the complainant to lead evidence in support of his allegations in the private complaint.
At the Congress "Chintan Shivir" in Jaipur, Shinde had accused the Bhrataiya Janata Pary (BJP) and its mentor, the Rashtriya Swayamsewak Sangh (RSS), of conducting terror training camps and promoting "Hindu terrorism".
Garg filed a complaint seeking registration of first information report (FIR) against Shinde for his remark against the BJP and the RSS.
The complaint accused Shinde of making "imputations prejudicial to national integration, uttering words with deliberate intent to wound religious feelings of Hindus, defaming them, and insulting their religion and beliefs".