Question: What is the national agency governing rail transportation in the Philippines?

Department of Transportation (Philippines)


The Department of Transportation (DOTr; Filipino: Kagawarán ng Transportasyon) is the executive department of the Philippine government responsible for the maintenance and expansion of viable, efficient, and dependable transportation systems as effective instruments for national recovery and economic progress.
The department is responsible for the country's land, air, sea communications infrastructure.
Until June 30, 2016, the department was named Department of Transportation and Communications (DOTC; Filipino: Kagawarán ng Transportasyón at Komunikasyón). With Republic Act No. 10844 or "An Act Creating the Department of Information and Communications Technology", signed into law on May 20, 2016 during the administration of Outgoing President Benigno Aquino III, the Information and Communications Technology Office was spun off the Department of Science and Technology (DOST) and merged with all operative units of the DOTC dealing with communications, to form the new Department of Information and Communications Technology.[2]
History
From 1899 to 1979 all transportation and communications activities were integrated into the structure and activities of what is now today the Department of Public Works and Highways.
Early history
On July 28, 1979, the Ministry of Transportation and Communications (MOTC), headed by Minister José P. Dans Jr. was formally created pursuant to Executive Order No. 546. Under this Executive Order, the Ministry of Public Works, Transportation and Communications (MPWTC) was divided into two separate ministries: The Ministry of Transportation and Communications (MOTC) and the Ministry of Public Works and Highways (MPWH).
The MOTC became the primary policy, planning, programming, coordinating, implementing and administrative entity of the executive branch of the government in the promotion, development and regulation of a dependable and coordinated network of transportation and communication systems.
The infrastructure projects undertaken during this period included:
Light Rail Transit System
Computer-Controlled Traffic Lights System
Manila International Airport, renamed to Ninoy Aquino International Airport
Central Post Offices in Makati, Caloocan, Quezon City, and San Juan
It was also during this period that the motor vehicle registration and control was improved with the introduction of permanent vehicle license plates and the staggered registration system. A bus leasing program provided an additional 1,000 new buses in Metro Manila.
The operations of both the Philippine National Railways and the Metro Manila Transit Corporation were improved and expanded. At the same time, the Manila South Line of the PNR serving the Bicol Region was rehabilitated.
Post-1986
On February 26, 1986, just after the 1986 EDSA Revolution, Congressman Hernando B. Pérez was appointed Minister of Transportation and Communication by President Corazon C. Aquino.
In March 1987, technocrat Rainerio O. Reyes, was appointed Minister of MOTC.  Immediately after, the MOTC was reorganized pursuant to Executive Order Nos. 125, and 125-A.  With these Executive Orders, the MOTC was made into a Department, under the Executive branch of the Government.
Under Secretary Reyes, the quasi-judicial functions of the Department were transferred to the Land Transportation Franchising and Regulatory Board, which was created through Executive Order No. 202.
Under Fidel V. Ramos
Jesus B. Garcia was appointed Secretary of the DOTC by President Fidel V. Ramos.  Under Garcia, new entrants were allowed in the landline and cellular phone services, dilapidated taxi cabs were also phased out in favor of brand new and late model units.
Present
By 2016, the foundation of the Department of Information and Communications Technology caused the DOTC to become simply the DOTr as the DICT transferred the DOTC's communications agencies to it.
On July 2017, the Agency began transferring its main operations from its longtime Headquarters at Columbia Tower in Mandaluyong to Clark, Mabalacat, Pampanga.[3]
Currently, the DOTr is expected to pursue numerous projects as part of President Rodrigo Duterte's promise to usher in a "Golden Age of Infrastructure"[4] with PHP 3.6T worth of public infrastructure projects being rolled out from 2018 to 2022.
Ongoing projects

Railways
Metro Manila Subway

The Metro Manila Subway, originally named Mega Manila Subway, is an approved underground rapid transit line to be built initially in Metro Manila in the Philippines. Construction is projected to begin by 2018, and to finish by 2025.[5]
LRT-2 East Extension

The LRT Line 2 East Extension Project, is the currently under-construction eastward extension of LRT Line 2, which adds 4-kilometer (2.5mi) of new line, starting from the eastern terminus of Santolan Station in Marikinaup to Masinag in Antipolo. The project aims to accommodate an additional 80,000 passengers and reduce traffic congestion along Marcos Highway. When the project is completed, it will reduce travel time from Recto to Masinag from 3 hours to only 40 minutes. It is scheduled to be finished by 2019
PNR North-South Commuter Rail
The North-South Commuter Rail is an under-construction commuter rail from New Clark City in Capas, Tarlac to Calamba, Laguna. The North Line will have a length of 106-kilometer, from Tutuban Station in Manila to New Clark City, and is expected to be completed by 2021.[6][7] The South Line will be reconstructed as an electrified standard-gauge full double-track line.
Pre-construction work such as clearing of the right of way have been started as of January 2018.
Organizational Structure
The  Department is headed by the Secretary of Transportation (Philippines), with the following seven undersecretaries and thirthteen assistant secretaries 
Undersecretary for Administration and Finance
Undersecretary for Road and Infrastructure
Undersecretary for Aviation and Airports
Undersecretary for Railways
Undersecretary for Legal Affairs and Procurement
Undersecretary for Planning and Project Development
Undersecretary for Maritime
Assistant Secretary for Legal Affairs
Assistant Secretary for Administration and Finance
Assistant Secretary for Aviation Intelligence and Enforcement
Assistant Secretary for Procurement
Assistant Secretary for Communications
Assistant Secretaries for Maritime
Assistant Secretaries for Road Transport and Infrastructure
Assistant Secretary for Railways
Assistant Secretaries for Planning
Assistant Secretary for Project Implementation
Attached agencies

Land (Road)
Land Transportation Office (LTO)
Land Transportation Franchising and Regulatory Board (LTFRB)
Toll Regulatory Board (TRB)
Rail
Philippine National Railways (PNR)
Light Rail Transit Authority (LRTA)
Metro Rail Transit Corporation Though MRTC is not under the government, the DOTr supervises the operation of the MRT-3 (MRTC)
North Luzon Railways Corporation (NORTHRAIL)
Air
Civil Aviation Authority of the Philippines (CAAP)
Civil Aeronautics Board (CAB)
Philippine Aerospace Development Corporation (PADC)
Manila International Airport Authority (MIAA-NAIA)
Mactan-Cebu International Airport Authority (MCIAA)
Sea
Maritime Industry Authority (MARINA)
Philippine Coast Guard (PCG)
Philippine Merchant Marine Academy (PMMA)
Philippine Ports Authority (PPA)
Cebu Port Authority (CPA)
Miscellaneous
Office for Transportation Security (OTS)
Office of Transportation Cooperatives (OTC)
Secretaries of Transportation