Former Department of Public Works and Highways (DPWH) Secretary Manuel “Manny” Bonoan appeared before the Sandiganbayan on Friday for arraignment in the remaining graft case tied to the alleged flood control kickback scandal, even as a separate court ruling has already removed him as an accused in two other cases.
The development comes just days after the Sandiganbayan Fifth Division granted the Office of the Ombudsman’s request to drop Bonoan from the plunder and graft cases involving former Sen. Jinggoy Estrada and three former DPWH officials.
Bonoan’s removal from those cases was part of the Ombudsman’s effort to use him as a state witness in other investigations involving alleged corruption in flood control projects.
One graft case remains
Despite his exclusion from the cases handled by the Sandiganbayan Fifth Division, Bonoan was not completely cleared of criminal charges.
The Sandiganbayan Second Division had earlier rejected prosecutors’ attempt to remove him from another graft case involving Estrada.
That case concerns allegations surrounding approximately P213.75 million in supposed kickbacks linked to two DPWH projects in Bulacan with a combined value of about P855 million.
In its August resolution, the Second Division said removing Bonoan after Estrada had already been arraigned could prejudice the senator because it would substantially change the prosecution’s theory of the case—from an alleged conspiracy involving both men to a case focused primarily on Estrada.
The court nevertheless clarified that the prosecution could still seek Bonoan’s discharge as a state witness at the proper stage of the proceedings, provided the requirements under the rules were satisfied.
Why Bonoan became a key government witness
The Ombudsman has sought Bonoan’s cooperation because prosecutors believe his knowledge of the DPWH system could help establish how allegedly anomalous flood control projects were inserted into government budgets and implemented.
Ombudsman Jesus Crispin Remulla previously said Bonoan possessed information that could be important in prosecuting other individuals involved in the broader flood control corruption investigation.
Bonoan had already appeared as a prosecution witness in another flood control-related case involving former senator Ramon “Bong” Revilla Jr. The case involved an allegedly nonexistent flood control project in Pandi, Bulacan.
From accused to potential state witness
The dramatic shift in Bonoan’s legal status followed the Ombudsman’s decision to seek his discharge from the cases where he had been charged alongside Estrada and former DPWH district officials Manny Bulusan, Arturo Gonzales Jr. and Denryl Caesar Cortuna.
The Fifth Division ultimately voted 2-1 to grant the prosecution’s request.
Associate Justice Gener Gito dissented, questioning whether the Ombudsman had adequately explained the details of Bonoan’s proposed immunity arrangement and arguing that important information about the agreement had not been sufficiently presented to the court.
The majority, however, held that determining which accused should be used as a state witness falls within the Ombudsman’s prosecutorial discretion.
Bonoan released from hospital arrest
The ruling also paved the way for Bonoan’s release from hospital detention.
The former DPWH chief had been under hospital arrest at the Philippine National Police General Hospital in Camp Crame since June because of his age and medical conditions.
The Sandiganbayan Fifth Division subsequently recalled the commitment orders against him and ordered his release, unless he was being detained for another lawful reason.
The PNP later confirmed that Bonoan was released from the hospital on Friday morning.
However, his release does not mean that every case against him has disappeared.
He still faces the separate graft charge before the Sandiganbayan Second Division, for which he had previously posted P90,000 bail.
Estrada’s case moves forward
Meanwhile, the proceedings involving Estrada also took a significant turn.
During his arraignment before the Fifth Division, Estrada declined to personally enter a plea. The court consequently entered a not-guilty plea on his behalf, in accordance with criminal procedure.
Estrada is accused of receiving hundreds of millions of pesos in alleged kickbacks connected to infrastructure and flood control projects under the 2025 national budget. His defense has indicated that it intends to challenge the court’s approval of the amendment that removed Bonoan as his co-accused.
Estrada has said he intends to pursue all available legal remedies concerning Bonoan’s exclusion from the case.
The bigger flood control investigation
The Bonoan proceedings form part of a much wider government investigation into alleged irregularities in flood control and infrastructure projects.
The allegations include claims of budget insertions, favored project allocations, questionable contracts and kickback arrangements involving government officials and private contractors.
Bonoan himself resigned as DPWH secretary in September 2025 following President Ferdinand Marcos Jr.’s directive for a broader investigation into alleged irregularities in flood control projects.
The former secretary has also been linked administratively to allegedly nonexistent flood control projects in Bulacan.
Malacañang has stressed that the President does not have authority to overturn the Sandiganbayan’s judicial decisions, citing the constitutional principle of separation of powers. The Palace has also maintained that those responsible for wrongdoing should be held accountable, while respecting due process and the independence of the courts and Ombudsman.
What happens next?
Bonoan’s legal situation is now unusually complicated.
He has been removed as an accused in the Fifth Division’s plunder and graft cases, released from hospital detention and positioned to cooperate with prosecutors as a potential state witness.
But he remains connected to a separate graft case before the Second Division, meaning his legal exposure has not completely ended.
The crucial question now is whether his testimony will become a major piece of evidence in the government’s wider flood control corruption cases—and whether his cooperation will ultimately withstand challenges from the other accused.
For now, the flood control scandal continues to unfold in court, with Bonoan occupying a pivotal position that could potentially shed more light on how the alleged scheme operated.
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