The Philippines until now has had one of the world's lowest minimum ages of sexual consent, behind Nigeria's age of 11, according to the United Nations Children's Fund (UNICEF).
A joint 2015 study by UNICEF and the Centre for Women's Resources, a local non-governmental group, showed seven of 10 rape victims in the Philippines were children.
One in five respondents age 13 to 17 reported experiencing sexual violence, while one in 25 experienced forced consummated sex during childhood, the study said.
Under the bill endorsed by Duterte, which is gender neutral, any adult engaging in sexual contact with anyone 16 or under would be committing statutory rape, unless the age difference between them was three years or less and sex was proven to be consensual, and neither abusive nor exploitative.
The exemption does not apply if the one of those involved was under 13.
"We welcome this legal development and hope that it will help protect young girls from rape and sexual abuse," said Josalee Deinla, spokesperson of the National Union of Peoples' Lawyers, which provides legal help to poor and marginalised people in the Philippines.
Lawrence Fortun, one of the bill's main sponsors, described it as "a major step forward".
"I am elated that our collective efforts at pushing for stronger protection against rape and other forms of sexual abuse are advancing," he said in a statement.
