Transportation Undersecretary Rene Limcaoco confirmed on 27 December 2013 that the proposed North-South commuter express line would be more expensive than the PHP 64.9bn (USD 1.45bn) Light Rail Transit (LRT) 1 Cavite Extension project, which is currently the single most expensive project of the government.

"If it gets National Economic Development Authority (NEDA) approval, it will be," Limcaoco told local press reporters during the inauguration of the Philippine National Railways’ new stations in Muntinlupa and Laguna.

Limcaoco, however, declined to disclose the cost of the ambitious project, saying the costing is "still subject to verification." Limcaoco is the alternate chairman of the PNR Board of Directors.

Transportation Secretary Joseph Emilio Abaya said the Japan International Cooperation Agency (JICA) is funding the feasibility study for the proposed North-South commuter express line, which will use the PNR’s right of way.

"The Malolos-Calamba line will cater mostly to the Greater Manila area. This line will be convenient for people who live in the provinces and work in Metro Manila. The Japan International Cooperation Agency (JICA) is helping us on this and the feasibility study is about to finish soon," he said.

Based on JICA’s proposed design, the 91.37-kilometer commuter express will have 27 stations. It will utilize elevated tracks from Malolos to Paco station in Manila. The mass transit line will then go underground from Buendia to FTI stations in Makati and Taguig, and will use elevated tracks again from Bicutan to Sucat stations. The commuter line will use at-grade tracks from Alabang in Muntinlupa to Calamba in Laguna.

The new commuter rail facility is envisioned to use train sets of 10 cars each and the maximum running speed will be 100 kilometers per hour. JICA is proposing that the new mass transit facility be operational for 18 hours a day up to midnight.

Abaya, however, said government is still studying whether to implement the project through public-private partnership (PPP) scheme or through Official Development Assistance (ODA) loan, considering the high cost of investment in a rail facility.

He said the project would be completed five or six years after awarding of contract.