Ong is accused for allegedly holding military intelligence agent Sgt. Vidal Doble against his will at the seminary.
The court said Ong was not treated fairly when the affidavits were ignored just because he and the others did not appear to affirm their sworn statements.
Pozon said the investigating panel actually took into consideration other affidavits.
"These prosecution witnesses likewise did not appear before the panel to affirm their respective statements," he said.
The judge gave weight to the affidavit of Bacani, who said Doble stayed at the seminary willfully."In sum, the affidavit of Bishop Bacani points to the fact that Vidal Doble Jr. was never detained contrary to allegations that he was seriously and illegally detained," he said.