The Kadapa MP opposed separate trial for each chargesheet on the ground that it violates Supreme Court orders in various cases.
Jaganmohan Reddy's lawyer argued that the court can begin the combined trial after the investigating agency completes the process of filing the chargesheets.
The CBI, however, informed the court that it was probing various aspects of the case and defended separate trial on each chargesheet.
The special court dealing with the Central Bureau of Investigation (CBI) cases adjourned the hearing on the petition till April 24.
Jagan, as the YSR party leader is popularly called, filed the petition after the court took cognizance of a supplementary chargesheet filed by the CBI April 2 against some pharma companies who invested in his firms.
The CBI has so far filed five chargesheets. In the latest chargesheet filed last week, it named home minister Sabitha Indra Reddy as an accused.
She is the third minister of Kiran Kumar Reddy to be named in the case, for allegedly showing favours to companies which made investments into Jagan's businesses.
Jagan has also filed a bail petition in the Supreme Court, and the same is likely to come up for hearing this case.
The MP, in his petition, argued that the latest chargesheet by the CBI violated the Supreme Court order.
He pointed out that the apex court in its order in October last year had directed the CBI to file a consolidated chargesheet.
This is the second time Jagan has moved the Supreme Court for bail. His earlier petition was dismissed in October last year.
The CBI court and also Andhra Pradesh High Court have also rejected his two bail petitions each.
The son of late chief minister YS Rajasekhara Reddy was arrested in May last year and is since lodged in the Chanchalguda jail here.
The CBI has charged him with entering into a criminal conspiracy with his father and then chief minister to dole out favours to companies and individuals who made investments in his businesses.
Several ministers, who also served in Rajaskehara Reddy's cabinet and officials are facing CBI probe for issuing controversial orders, allotting land, granting mining licenses and other favours to various companies.