The incident happened around 4:00 pm in a village at the church's global headquarters in Gapyeong east of Seoul, a church spokesman said.
The Japanese woman and a male church minister, who came together from Japan to mark the first anniversary of the death of Sun Myung Moon, suffered burns and are in serious condition in hospital, he said.
Another woman was slightly injured after being trapped in the fire.
He said the woman was reportedly mentally unstable and it was unclear whether she had intended to set herself and her male colleague on fire.
Foreign and local church members have been staying at the church's headquarters before a memorial service for Moon tomorrow.
Church officials said the service would draw more than 20,000 members, including about 6,000 Japanese.
Moon died at the age of 92 on September 3 last year, but followers observe August 23 as the first anniversary of his passing according to the lunar calendar.
Moon, revered by his followers but described by critics as a charlatan who brainwashed church members, was a deeply divisive figure whose shadowy business dealings once saw him jailed in the United States.
The teachings of the Unification Church are based on the Bible but with new interpretations. Moon saw his role as completing the unfulfilled mission of Jesus to restore humanity to a state of "sinless" purity.
While the church claims a worldwide following of three million, experts suggest the core membership is far smaller.
The church, whose members were mocked as "Moonies" by the media, was renowned for its mass weddings of thousands -- sometimes tens of thousands -- of couples and for its multi-billion-dollar business interests.
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