MANILA, Philippines — Former Department of Public Works and Highways (DPWH) Secretary Manuel Bonoan pleaded not guilty on Friday, September 4, to the remaining graft charge against him before the Sandiganbayan Second Division, as the legal fallout from the government’s sprawling flood control corruption investigation continues.
Bonoan personally entered his plea during his arraignment after his lawyer, Stephanie Ong, waived the reading of the formal charge. The court then proceeded with preliminary pretrial matters.
The development came only hours after Bonoan was released from hospital detention following a separate Sandiganbayan ruling that removed him as an accused in the plunder and graft cases pending before the court’s Fifth Division.
That distinction is crucial: Bonoan’s release did not mean all cases against him had disappeared. He remained an accused in the separate graft case before the Second Division, where he had already posted bail.
What is the remaining graft case about?
The Second Division case concerns allegations that Bonoan conspired with Sen. Jose “Jinggoy” Estrada in connection with the inclusion of flood control projects in Bulacan in the 2025 national budget.
According to prosecutors, the projects had a combined value of about P855 million, with Estrada allegedly receiving a P213.7-million kickback, equivalent to roughly 25% of the project amount.
The allegations remain accusations and have yet to be proven in court. Bonoan’s not-guilty plea means the case will proceed through the judicial process, where prosecutors must establish the charges with evidence.
Why was Bonoan released from detention?
The release followed a separate ruling by the Sandiganbayan Fifth Division that allowed prosecutors to remove Bonoan as an accused in the plunder and graft cases before that division.
The Fifth Division voted 2-1 to grant the Ombudsman’s request, ruling that choosing an accused to potentially serve as a state witness falls within the Ombudsman’s prosecutorial discretion.
The Ombudsman had sought Bonoan’s cooperation because of his claimed knowledge of the alleged flood control scheme and his willingness to provide information that could help investigators identify other individuals involved.
Bonoan had earlier offered to become a state witness and provide what his camp described as a comprehensive account of the alleged scheme. The Ombudsman said his cooperation could potentially help investigators understand how the alleged operation worked and identify higher-ranking officials or private individuals who may have participated.
However, the Second Division previously rejected the prosecution’s attempt to discharge Bonoan from the separate graft case.
In August, the court ruled that removing him from that case could prejudice Estrada’s defense because Estrada had already been arraigned and Bonoan’s alleged participation could be relevant to determining the respective roles of those accused.
The prosecution subsequently sought reconsideration of that ruling.
Bonoan’s legal situation is now split between two court proceedings
The result is an unusual legal situation.
Bonoan is no longer an accused in the Fifth Division’s plunder and graft cases, allowing authorities to release him from hospital arrest. But he remains an accused in the Second Division’s graft case, where he pleaded not guilty Friday.
The Philippine Star reported that Bonoan had been held at the Philippine National Police General Hospital in Camp Crame under hospital arrest after a warrant was issued against him in May.
His release followed the Fifth Division’s decision to recall the commitment orders after removing him from the cases before that division.
GMA News likewise reported that Bonoan’s convoy left the PNP General Hospital on Friday morning after authorities verified that he had no other warrant that would prevent his release.
The wider flood control investigation
The case against Bonoan forms part of a much larger government investigation into alleged irregularities surrounding flood control and infrastructure projects.
The Office of the Ombudsman filed plunder and graft cases in May against Estrada, Bonoan and other former DPWH officials over alleged kickbacks totaling about P573 million.
The prosecution alleged that public funds were directed toward selected infrastructure projects in exchange for predetermined commissions or kickbacks.
Several other officials originally linked to the case have also figured in the government’s efforts to build its evidence, including individuals who sought or were considered for state-witness status.
The Ombudsman’s decision to seek Bonoan’s cooperation has attracted considerable attention because investigators believe a former DPWH secretary could potentially provide information about how project allocations, contractors and alleged kickbacks were handled.
What happens next?
With Bonoan now having entered a not-guilty plea in the Second Division case, the proceedings move toward the pretrial stage.
Inquirer.net reported that Bonoan’s defense was not yet ready to submit its pretrial brief because it was still waiting for the court to resolve its motion for reconsideration concerning his continued inclusion in the case. The court nevertheless proceeded with preliminary matters, including the stipulation of facts.
Meanwhile, Estrada has indicated that he intends to pursue available legal remedies challenging the developments involving Bonoan’s removal from the separate Fifth Division cases.
For Bonoan, therefore, Friday’s plea was not the end of the flood control controversy surrounding him. It marked another significant turn in a case that is now unfolding across separate proceedings—with his possible role as a government witness in some investigations existing alongside his status as an accused in the remaining graft case.
And that distinction could become increasingly important as prosecutors attempt to determine who allegedly knew what, who made the decisions, and where the money involved in the alleged flood control scheme ultimately went.
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