The court agreed with the ED's argument that the cases registered by both the Central Bureau of Investigation (CBI) and the ED should be tried simultaneously.
Reddy, who personally appeared in the court on January 10, had moved the petition, pleading the court to take up hearing into the ED cases only after completing the hearing in the CBI cases.
The court also struck down the YSR Congress Party (YSRCP) President's petition of clubbing all the charge sheets filed in the case.
Reddy, who had made first personal appearance in the court since assuming office as the Chief Minister in May last year, had sought exemption from personal attendance this week. The CBI court hears the case every Friday.
The court on Friday began hearing on the charge sheet in the Penna Cement case, one of 11 cases registered by the federal agency. All the other accused in the case appeared in the court. They included Telangana Minister Sabita Indra Reddy, YSR Congress MP V. Vijaya Sai Reddy, former Andhra Pradesh Minister Dharmana Prasada Rao and IAS officer Srilakshmi.
The cases relate to investments made by various companies in Jagan's firms as quid pro quo for various favours bestowed on them during the tenure of his father, the late Y.S Rajasekhara Reddy, as Chief Minister of undivided Andhra Pradesh during 2004 and 2009.
The CBI arrested Reddy and sent him to jail on May 27, 2012. After 16 months in prison, he was granted bail.
The federal agency has filed 11 chargesheets against Jagan and others.
( With inputs from IANS )