See - http://sc.judiciary.gov.ph/jurisprudence/2010/april2010/186450.htm
NATIONAL WATER RESOURCES BOARD (NWRB) vs. A. L. ANG NETWORK, INC.,
G.R. No. 186450, April 8, 2010.
"In issue is whether Regional Trial Courts have jurisdiction over appeals from decisions, resolutions or orders of the National Water Resources Board (petitioner).
Petitioner maintains that the RTC does not have jurisdiction over a petition for certiorari and prohibition to annul or modify its acts or omissions as a quasi-judicial agency. Citing Section 4 of Rule 65 of the Rules of Court, petitioner contends that there is no law or rule which requires the filing of a petition for certiorari over its acts or omissions in any other court or tribunal other than the Court of Appeals.
Petitioner goes on to fault the appellate court in holding that Batas Pambansa Bilang 129 (BP 129) or the Judiciary Reorganization Act did not expressly repeal Article 89 of Presidential Decree No. 1067 (PD 1067) otherwise known as the Water Code of the Philippines.
Respondent, on the other hand, maintains the correctness of the assailed decision of the appellate court.
The petition is impressed with merit.
Section 9 (1) of BP 129 granted the Court of Appeals (then known as the Intermediate Appellate Court) original jurisdiction to issue writs of mandamus, prohibition, certiorari, habeas corpus and quo warranto, and auxiliary writs or processes, whether or not in aid of its appellate jurisdiction.
Since the appellate court has exclusive appellate jurisdiction over quasi-judicial agencies under Rule 43 of the Rules of Court, petitions for writs of certiorari, prohibition or mandamus against the acts and omissions of quasi-judicial agencies, like petitioner, should be filed with it. This is what Rule 65 of the Rules imposes for procedural uniformity. The only exception to this instruction is when the law or the Rules itself directs otherwise, as cited in Section 4, Rule 65. The appellate courts construction that Article 89 of PD 1067, which reads:
ART. 89. The decisions of the [NWRB] on water rights controversies may be appealed to the [RTC] of the province where the subject matter of the controversy is situated within fifteen (15) days from the date the party appealing receives a copy of the decision, on any of the following grounds: (1) grave abuse of discretion; (2) question of law; and (3) questions of fact and law (emphasis and underscoring supplied),
is such an exception, is erroneous.
Article 89 of PD 1067 had long been rendered inoperative by the passage of BP 129. Aside from delineating the jurisdictions of the Court of Appeals and the RTCs, Section 47 of BP 129 repealed or modified:
x x x. [t]he provisions of Republic Act No. 296, otherwise known as the Judiciary Act of 1948, as amended, of Republic Act No. 5179, as amended, of the Rules of Court, and of all other statutes, letters of instructions and general orders or parts thereof, inconsistent with the provisions of this Act x x x. (emphasis and underscoring supplied)
The general repealing clause under Section 47 predicates the intended repeal under the condition that a substantial conflict must be found in existing and prior acts.
In enacting BP 129, the Batasang Pambansa was presumed to have knowledge of the provision of Article 89 of P.D. No. 1067 and to have intended to change it. The legislative intent to repeal Article 89 is clear and manifest given the scope and purpose of BP 129, one of which is to provide a homogeneous procedure for the review of adjudications of quasi-judicial entities to the Court of Appeals.
More importantly, what Article 89 of PD 1067 conferred to the RTC was the power of review on appeal the decisions of petitioner. It appears that the appellate court gave significant consideration to the ground of grave abuse of discretion to thus hold that the RTC has certiorari jurisdiction over petitioners decisions. A reading of said Article 89 shows, however, that it only made grave abuse of discretion as another ground to invoke in an ordinary appeal to the RTC. Indeed, the provision was unique to the Water Code at the time of its application in 1976.
The issuance of BP 129, specifically Section 9 (Jurisdiction of the Court of Appeals, then known as Intermediate Appellate Court), and the subsequent formulation of the Rules, clarified and delineated the appellate and certiorari jurisdictions of the Court of Appeals over adjudications of quasi-judicial bodies. Grave abuse of discretion may be invoked before the appellate court as a ground for an error of jurisdiction.
It bears noting that, in the present case, respondent assailed petitioners order via certiorari before the RTC, invoking grave abuse of discretion amounting to lack or excess of jurisdiction as ground-basis thereof. In other words, it invoked such ground not for an error of judgment.
While Section 9 (3) of BP 129 and Section 1 of Rule 43 of the Rules of Court does not list petitioner as among the quasi-judicial agencies whose final judgments, orders, resolutions or awards are appealable to the appellate court, it is non sequitur to hold that the Court of Appeals has no appellate jurisdiction over petitioners judgments, orders, resolutions or awards. It is settled that the list of quasi-judicial agencies specifically mentioned in Rule 43 is not meant to be exclusive. The employment of the word among clearly instructs so.
BF Northwest Homeowners Association v. Intermediate Appellate Court, a 1987 case cited by the appellate court to support its ruling that RTCs have jurisdiction over judgments, orders, resolutions or awards of petitioner, is no longer controlling in light of the definitive instruction of Rule 43 of the Revised Rules of Court.
Tanjay Water District v. Gabaton is not in point either as the issue raised therein was which between the RTC and the then National Water Resources Council had jurisdiction over disputes in the appropriation, utilization and control of water.
IN FINE, certiorari and appellate jurisdiction over adjudications of petitioner properly belongs to the Court of Appeals.
WHEREFORE, the challenged Decision and Resolution of the Court of Appeals are REVERSED and SET ASIDE. The April 15, 2005 Order of the Regional Trial Court of Bacolod City dismissing petitioners petition for lack of jurisdiction is UPHELD.
x x x."
 SEC. 9. Jurisdiction.The [Court of Appeals] shall exercise:
(1) Original jurisdiction to issue writs of mandamus, prohibition, certiorari, habeas corpus, and quo warranto, and auxiliary writs or processes, whether or not in aid of its appellate jurisdiction.;
(2) Exclusive original jurisdiction over actions for annulment of judgments of Regional Trial Courts; and
(3) Exclusive appellate jurisdiction over all final judgments, decisions, resolutions, orders or awards of Regional Trial Courts and quasi-judicial agencies, instrumentalities, boards or commissions, except those falling within the appellate jurisdiction of the Supreme Court in accordance with the Constitution, the provisions of this Act, and of subparagraph (1) of the third paragraph and subparagraph (4) of the fourth paragraph of Section 17 of the Judiciary Act of 1948.
x x x x.
 SECTION 1. Scope.This Rule shall apply to appeals from judgments or final orders of the Court of Tax Appeals* and from awards, judgments, final orders or resolutions of or authorized by any quasi-judicial agency in the exercise of its quasi-judicial functions. Among these agencies are the Civil Service Commission, Central Board of Assessment Appeals, Securities and Exchange Commission,** Office of the President, Land Registration Authority, Social Security Commission, Civil Aeronautics Board, Bureau of Patents, Trademarks and Technology Transfer, National Electrification Administration, Energy Regulatory Board, National Telecommunications Commission, Department of Agrarian Reform Under Republic Act No. 6657, Government Service Insurance System, Employees Compensation Commission, Agricultural Inventions Board, Insurance Commission, Philippine Atomic Energy Commission, Board of Investments, Construction Industry Arbitration Commission, and voluntary arbitrators authorized by law.
x x x x (underscoring supplied)
 SEC. 4. When and where to file the petition. x x x .
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. It may also be filed with the Court of Appeals or with the Sandiganbayan, whether or not the same is in aid of the courts appellate jurisdiction. If it involves the acts of a quasi-judicial agency, unless otherwise provided by law or these rules, the petition shall be filed in and cognizable only by the Court of Appeals.
x x x x. (emphasis and underscoring supplied)
 Mecano v. Commission on Audit, G.R. No. 103982, 216 SCRA 500, 505 (1992).
 Vide: Magno v. Commission on Elections, G.R. No. 147904, 390 SCRA 495, 500 (2002).
 Vide: United Coconut Planters Bank v. E. Ganzon, Inc, G.R. Nos. 168859 and 168897, June 30, 2009, 591 SCRA 321, 337; Land Bank of the Philippines v. De Leon, 437 Phil. 347, 357 (2002); Sy v. COSLAP, 417 Phil. 378, 393-394 (2001); and Metro Construction, Inc. v. Chatham Properties, Inc., 418 Phil. 176, 203 (2001).
 G.R. No. 72370, 234 Phil. 537 (1987).
 G.R. No. 63742, 254 Phil. 253 (1989).