In a 24-page resolution, Presiding Justice Francis Garchitorena, who chairs the anti-graft courts first division, said the prosecution has not shown a well-founded justification for the withdrawal of the graft case against Estrada and his co-accused.
At the same time, Garchitorena also ordered the prosecution to submit the evidence at preliminary investigation in support of the information of the charges it has filed before the court.
Garchitorena said the duty of the prosecutors to charge all who appear to be responsible for an offense is not left to the preferences of the prosecutors.
"Once there is adequate evidence at preliminary investigation, what arises is the duty and obligation of the prosecutor to charge all persons to whom adequate evidence points. This is mandatory and is enforceable by mandamus," Garchitorena said.
"As part of that duty, in the filing of the information, the prosecution must accompany the information with the affidavits and counter-affidavits filed as well as with other supporting evidence and resolution of the case," he added.
Aside from the Estradas, also accused are Charlie "Atong" Ang, Eleuterio Tan, Alma Alfaro and a certain Delia Rajas.
The graft case, docketed as criminal case 26561, stemmed from Estradas alleged skimming of P130 million in tobacco excise taxes of Ilocos Sur which he shared with Mrs. Ejercito, Jinggoy and Ang.
Meanwhile, Ombudsman Aniano Desierto asked the Sandiganbayans third division to arraign the former president and his son on the capital charge of plunder on June 18 together with lawyer Edward Serapio and five others.
Desierto said the prosecution will be presenting evidence and witnesses on the scheduled June 18-26 bail hearings for Serapio to prove that the guilt of the accused in the plunder case is strong.
"To avoid repetitions of the presentation of the evidence and witnesses in the plunder case, we urge this honorable court to also conduct the arraignment of all the accused in the plunder case. Trial must be expedited immediately to enable the court to spend lesser effort, time and money," Desierto said.
Desierto said the joint arraignment of Estrada, Jinggoy, Serapio, Ang, Tan, Rajas, Alfaro, Yolanda Ricaforte and a Jane and John Doe on June 18 will also spare the police from further security risks.
He noted that the underlying purpose of the law disallowing bail in capital offense is to prevent the escape from the law of persons charged with crimes punishable by life imprisonment or death. "Records of the Sandiganbayan itself showed more than 200 cases in which the accused had escaped prior to his arraignment," Desierto argued.