The Sandiganbayan First Division has denied prosecutors' request to dismiss former Department of Public Works and Highways (DPWH) Secretary Manuel Bonoan from the graft case against Sen. Jinggoy Estrada, ruling that doing so after Estrada's arraignment would prejudice the senator's rights.

In a 12-page resolution dated 3 August, the anti-graft court said it could not grant the prosecution's motion to amend the information because Estrada had already been arraigned under the original charges.

The court cited Supreme Court jurisprudence holding that while the State has an interest in prosecuting crimes, that interest must be balanced against an accused person's procedural rights.

"The Supreme Court has consistently held that while the State has an interest in the prosecution of offenses, such interest must be balanced against the accused's fundamental procedural rights. Once arraigned, an accused is entitled to rely on the allegations contained in the information to which he entered a plea," the resolution stated.

The court added that removing Bonoan as a co-accused at this stage could limit the defenses available to Estrada.

"At this stage of the proceedings, the Court finds that the exclusion of accused Bonoan would unduly restrict the defenses available to accused Estrada. Accused Bonoan's participation as a co-accused may bear upon the presentation of evidence."

The Sandiganbayan also ruled that the proposed amendment was substantial, not merely formal.

A formal amendment corrects minor errors that do not alter the nature of the charge, while a substantial amendment changes the legal theory or nature of the offense.

The court said removing Bonoan from the case would constitute a substantial amendment that could prejudice Estrada's rights.

However, the First Division clarified that its ruling should not be interpreted as a rejection of Bonoan's possible role as a state witness. It said prosecutors remain free to seek his dismissal at the appropriate stage of the proceedings.

Bonoan's role as a potential state witness

The Office of the Ombudsman has said it sought Bonoan's discharge to strengthen its broader investigation into the alleged multibillion-peso flood control anomaly, in which former House Speaker Martin Romualdez has been identified by investigators as one of the alleged masterminds.

Ombudsman Jesus Remulla said on 30 June that the office had reached a "standing agreement" with Bonoan because of his knowledge of the alleged scheme and his ability to testify in other flood control cases.

"The knowledge that he has about the whole institution is something very important to us to be able to prove other cases... we will be benefitting from his testimony with regards to so many of the cases we are filing," Remulla said.

More recently, however, the Ombudsman disclosed that it was reconsidering whether to pursue Bonoan's discharge after determining that he was allegedly withholding information from investigators.

Remulla warned that if Bonoan fails to fully cooperate, the Ombudsman may proceed with the criminal case against him.

"There are questions that he isn't answering properly. Of course, we're still trying to get everything he can contribute when there are some answers we're not able to get from him," he said.

A similar motion seeking Bonoan's dismissal has also been filed before the Sandiganbayan Fifth Division, which is handling the plunder case against Estrada, Bonoan and other former DPWH officials.