Mr Duterte was speaking to a crowd in South Korea when he called the woman on stage then convinced her to kiss him.
The scene drew cheers from the crowd, mostly made of up other Philippine workers.
But it was described as "disgusting theatrics of a misogynist president" by Philippines rights group Gabriela.
It is not the first time he has been accused of inappropriate behaviour towards women.
A history of misogyny
The controversial incident took place when Mr Duterte was speaking to a crowd of overseas Filipino workers (OFWs) in Seoul.
Two Philippine women were invited to join the president on stage to receive a free copy of a book, and were visibly star struck standing next to Mr Duterte.
He hugged the first and gave her a kiss on the cheek before gesturing the second woman to kiss him on the lips.
After a protracted back and forth, with nervous laughter from the young woman and repeated gestures by Mr Duterte, the president eventually leaned in to kiss the woman on the lips.
While the young woman was laughing and the crowd cheering, comments on the internet were a lot more critical.
Mr Duterte has sparked outrage before with a string of comments seen as misogynistic.
In April 2016, he spoke to an election campaign rally about the 1989 murder and rape of a female Australian missionary in Davao, where he was mayor at the time.
"I was angry because she was raped," he said. "That's one thing. But she was so beautiful, the mayor should have been first, what a waste." His office later apologised for the comments.
Earlier this year Mr Duterte told Filipino soldiers they should shoot female communist rebels in the vagina.
Both incidents lead to strong criticism and a backlash on social media.
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