MANILA— The Sandiganbayan Second Division has rejected the government prosecutors’ bid to discharge former Department of Public Works and Highways (DPWH) Secretary Manuel Bonoan as a co-accused in the graft case involving Senator Jinggoy Estrada over an alleged flood control kickback scheme.

The court informed the parties of its decision during Tuesday’s pre-trial conference in the case against Estrada and his co-accused.

Following the ruling, government prosecutors told the court that they would continue to treat Bonoan as an accused while awaiting further instructions from their superiors at the Office of the Ombudsman.

The Second Division’s action contrasts with the ruling of the Sandiganbayan Fifth Division, which earlier granted the prosecution’s request to remove Bonoan as an accused in the P573-million plunder case and a separate graft case tied to the alleged flood control kickback scheme.

The Fifth Division ruled 2-1 that the Ombudsman’s decision on whom to seek as a state witness falls within its “prosecutorial discretion.”

“The decision to move for the discharge of an accused is part of the Ombudsman’s prosecutorial discretion of who should be used as a state witness, to bolster the successful prosecution of criminal offenses,” the Sandiganbayan said.

The division also held that the Ombudsman has the authority under the law to grant immunity to a state witness.

The Ombudsman had sought Bonoan’s exclusion from the cases in June after he expressed willingness to cooperate with the agency. It said his testimony was needed to expose the alleged system behind kickbacks from anomalous flood control projects.

“His cooperation was indispensable to uncover the architecture that may have set the entire machinery in motion,” the Ombudsman said in its June 11, 2026 resolution.

The prosecution wanted Bonoan discharged so he could testify as a state witness in other flood control cases, including the master case involving an alleged scheme to defraud the national government involving former House Speaker Martin Romualdez.

Bonoan was among Estrada’s co-accused, along with three others, in charges filed by the Ombudsman in May over an alleged conspiracy to collect more than P500 million in kickbacks from flood control projects.

The former DPWH chief had also testified in the malversation and graft cases involving former Senator Ramon “Bong” Revilla Jr., where he disclosed the so-called Leadership Fund, an ad-hoc allocation for priority projects of senators.

The Fifth Division’s ruling resulted in the recall of the warrant of arrest and hold departure order against Bonoan, as well as his release from hospital detention on September 3.

The Second Division, however, had earlier rejected a similar prosecution motion involving Bonoan in a separate graft case.

In an Aug. 3 resolution, the Second Division said removing Bonoan could prejudice Estrada by changing the prosecution’s theory of criminal liability and limiting the defenses available to the senator, who had already entered a plea based on the original allegations.

Estrada’s counsel, Atty. Laurence Arroyo, had opposed the prosecution’s bid to discharge Bonoan, arguing that his removal as a co-accused would prejudice the senator’s rights and fundamentally alter the prosecution’s theory of conspiracy.

Bonoan had previously posted bail for his graft case before the Second Division.

The graft case concerns alleged partiality that resulted in injury to the government. Under the law, plunder involves a public officer who, through a combination or series of overt or criminal acts, amasses ill-gotten wealth totaling at least P50 million.

A 2016 Supreme Court ruling requires the prosecution to establish a principal plunderer for a conviction.

Estrada said he respects the Fifth Division’s ruling but intends to pursue the legal remedies available to him.

“While I respect the decision of the Sandiganbayan, I wish to emphasize that there remain legal remedies available to me under our judicial system, which my legal team will carefully study and pursue at the appropriate time,” he said.

“This development does not end my legal recourse, and I will continue to place my trust in due process and the rule of law,” Estrada said.

“My faith in our judicial system remains firm. I will continue to stand by the truth and pursue every lawful means available to protect my rights and clear my name and honor,” he added.