He pecked one of two women who came up onto the stage on the cheek, but then gestured to the other that he wanted to kiss her on the lips.
The president could be heard saying: "Are you single? You're not separated from him? But you can tell him that this is just a joke?" reported Rappler.
His awkward move drew cheers from the audience, but his claims that it was only a gimmick did not prevent a backlash online where Mr Duterte was slammed for being a "misogynist" and a "hypocrite."
Women's rights group Gabriela said in a statement: "His repeated acts of machismo are meant as entertainment to hide the reality of his rapidly slipping popularity due to the issues of extrajudicial killings, the Tax Reform for Acceleration and Inclusion law and big-time corruption scandals now plaguing his rule."
One Twitter user added: "I'm not even going to state all the things that's obviously wrong here. But look at how President Duterte is gripping the Filipina's forearms while he kisses her in front of an audience."
"President DUTERTE said at the end of his speech in South Korea that the "KISS" was only for entertainment. Hah! I'm not buying it Mr President. The woman was not an entertainer. Advancing on women for entertainment purpose is OFFENSIVE," said another.
The presidential palace has insisted that Duterte is committed to women's rights, pointing to policies in his home city of Davao, where he served as a long-time mayor, that protect women from harassment.
However, Mr Duterte's attempts at humour may have fallen flat because of his long history in making sexist and derogatory remarks about women.
In a speech to soldiers in February, he made a crass quip that a new order would be given to shoot female rebels in the vagina.
Earlier that month he stated that he did not like foreign women because they had a "queer" odour, which helped him to remain faithful to more "fragrant" Filipina women.
In one of his most outrageous remarks, on the campaign trail for the 2016 election, Mr Duterte regretted that he did not get to go first in the gang-rape of Australian missionary, Jacqueline Hamill, who died during a 1989 hostage-taking incident in Davao.
"I was angry because she was raped, that's one thing. But she was so beautiful, the mayor should have been first, what a waste," he said.
He later apologised for his comments saying he had "no intention of disrespecting women," clarifying that "sometimes my mouth can get the better of me."
