Short answer. The Regional Trial Court exercising jurisdiction over the territorial area as defined by the Supreme Court. The rule adds that such a petition may also be filed with the Court of Appeals or the Sandiganbayan, whether or not in aid of that court's appellate jurisdiction.
What the law says
If the petition relates to an act or an omission of a municipal trial court or of a corporation, a board, an officer or a person, it shall be filed with the Regional Trial Court exercising jurisdiction over the territorial area as defined by the Supreme Court.
Rule 65, Section 4 — When and where to file the petition. Read the full provision →
One category covering more than courts
The clause groups four things together: a municipal trial court, a corporation, a board, and an officer or person. They are treated alike for this purpose, which is useful to know if your grievance is against a body rather than a judge. The forum for all of them is the Regional Trial Court, identified not at large but as the one exercising jurisdiction over the territorial area as defined by the Supreme Court. Territory, not convenience, selects the court.
The Regional Trial Court is not the only option
The rule then adds that the petition may also be filed with the Court of Appeals or with the Sandiganbayan, whether or not the same is in aid of the court's appellate jurisdiction. That is a genuine alternative rather than a fallback for when the first is unavailable. The closing words matter too: the qualification about being in aid of appellate jurisdiction is expressly removed, so a petitioner need not establish that connection to file in those courts.
A different rule for quasi-judicial agencies
Do not carry this answer across to every government body. The same provision deals separately with a quasi-judicial agency, and there the petition must be filed with, and is cognizable only by, the Court of Appeals unless otherwise provided by law or the rules. So the question of which forum applies turns on what the respondent actually is. Characterising the body correctly at the outset is not a formality; it decides where the petition belongs.
Election cases are carved out
There is one more exception in the same section, and it is easy to miss. In election cases involving an act or omission of a municipal or a regional trial court, the petition shall be filed exclusively with the Commission on Elections, in aid of its appellate jurisdiction. Given that filing in the wrong forum wastes a period that is already short, it is worth confirming with a lawyer both what the respondent is and where the petition goes before preparing it.