President Ferdinand Marcos Jr. lost confidence in former Public Works Secretary Manuel Bonoan over anomalous flood control projects that occurred under his watch, Malacañang said Wednesday.

Palace Press Officer Claire Castro made the statement after being asked about Bonoan’s testimony before the Sandiganbayan that Marcos had asked him to step down from the Department of Public Works and Highways.

Castro said Bonoan’s account was not inconsistent with the Palace’s earlier explanation that he left the department under the principle of command responsibility.

“It is not contradictory,” Castro said during the 2 September Palace press briefing.

She said that if Bonoan was admitting that Marcos had asked him to leave, this could still be understood in the context of the irregularities that emerged during his tenure at the DPWH.

“[Former] Secretary Manny Bonoan probably felt at the time that the President had lost confidence in him because this fell under his command responsibility,” Castro said.

“So, he had to resign and leave his position,” she added.

The Palace statement sharpened its previous framing of Bonoan’s departure, which had focused on command responsibility, by directly linking it to the President’s apparent loss of confidence in his former Cabinet official.

Bonoan has since figured prominently in proceedings related to the flood control controversy.

During the same briefing, Castro was asked about the Sandiganbayan’s decision to drop graft cases against Bonoan and concerns that the development could be interpreted as selective justice.

She said the Palace would respect the court’s ruling, stressing that the judiciary operates independently from the executive branch.

“Whatever decision the Sandiganbayan made in this case is already beyond the authority of the President,” Castro said.

She added that Marcos’ position remained that those responsible for wrongdoing should be held accountable regardless of political affiliation or personal ties.

Asked about the possibility of Bonoan becoming a state witness, Castro said the decision rested with the Ombudsman and that Malacañang had no information on the considerations behind it.

She said the anti-graft body may have determined that Bonoan’s testimony would be more useful in pursuing other respondents, but emphasized that this was for the Ombudsman to assess.

The Palace also rejected suggestions that the investigation was being directed against specific political personalities, saying those accused would have the opportunity to present evidence and defend themselves.

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