Duterte, who is known for his populist leanings, believes the long-term benefits of the measure outweigh the short-term budgetary challenges, said deputy presidential executive secretary Menardo Guevarra.
"Free tertiary education in state universities and colleges is a very strong pillar or cornerstone of the president's social development policy," he told reporters.
The bill, signed late yesterday, will spare all students at government-run colleges and universities from paying tuition and other fees, he added.
Guevarra said that now the measure had been signed, everyone needed to work together to solve the key problem facing the new bill: funding.
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"Everyone including the economic managers will have to focus their attention on this particular aspect: funding for this programme," he added.
Congressman Salvador Belaro, one of the authors of the bill for free state college tuition, warned it could cost some 500 billion pesos to fund the program through to 2022.
This is out of a total education budget of 691.1 billion pesos, budget department documents showed.
The Duterte government is already scrambling to cover its proposed 3.767 trillion peso budget for 2018, which includes heavy spending on infrastructure.