The reproductive health bill will, if passed by the two houses of Congress, guarantee access to free birth control and promote sex education.
The government says it will prevent further over population and create a more productive labour force.
Budget Secretary Florencio Abad says although Mr Aquino is a Catholic, like 80 per cent of the Philippines population, the bill has his backing.
"The president has already, at the risk of alienating the church, declared that the bill is a priority," he said.
"That message is very clear."
Contraceptives are generally available in the Philippines although they are not used as much as elsewhere.
In the Philippines, 45-50 percent of women of reproductive age, or their partners, are using a contraceptive method at any given time.
Indonesia's rate is 56 percent and Thailand's 80 percent.
Economists say the combination of a growing population and rampant poverty is causing Philippines to lag behind its booming neighbours.
But Catholic bishop Father Melvin Castro says the church disagrees.
"They are poor not because they have no access to contraceptives but because they have no work," he said.
"Give them work and it will be the most effective birth spacing means for them."
Family planning was enshrined in the Philippines constitution by dictator Ferdinand Marcos in 1973.
That clause was removed when it was rewritten in 1987, under the leadership of Mr Aquino's mother Corazon Aquino.
Despite the opposition, a poll last year showed about 70 per cent of people support the bill.
Its backers want it passed during the term of this congress, which ends in June.