The victim's sister contacted Cetri -- a nonprofit organization working in the field of social justice and international development -- in October to inform its members of the abuse, said Bernard Duterme, the organization's director.
In early November, Houtart resigned from the board of Cetri, which he had founded in the 1970s, Duterme said.
Houtart, who is currently in Ecuador, didn't immediately respond to phone calls and e-mail Wednesday, but in an interview with Belgian newspaper Le Soir, he is quoted as saying he twice touched "the intimate parts" of a boy he describes as his cousin 40 years ago. He calls the incident "inconsiderate and irresponsible."
The woman, however, reportedly claimed that he raped her brother twice.
The Catholic church in Belgium has been rocked by a sex abuse scandal and in June published a detailed report with the harrowing accounts of more than 100 victims. The abused included children aged between the ages of two and six years old.
In the interview, Houtart said the sister also contacted the committee campaigning to have him nominated for the Nobel Price. "The message from my cousin was a warning that only I could understand," Houtart is quoted as saying. He describes how he entered the boy's room when he was staying with the boy's parents close to Liege, in eastern Belgium.
"Walking through the room of one of the family's boys, I effectively touched his intimate parts twice, which woke him up and frightened him," Houtart is quoted as saying.
The committee in November ended its campaign to nominate Houtart for the 2011 Nobel Prize, saying the priest had requested its termination because "his age and his personal projects would not allow him to fully assume the role requested in such circumstances."
In a statement, the committee said "thousands of people" in 74 countries had participated in the signature campaign, recognizing Houtart's role in the social justice and antiglobalization movement.
According to Le Soir, the victim's sister is one of the witnesses in the report. In the section referred to by the paper, a woman details the abuse of her brother, which she describes as "rape."
She says the priest, who was a friend of her father, entered her brother's room twice "to rape him." "Before the third time, my brother went to tell his parents, who kept him in their room," she is quoted as saying in the report.
The priest isn't named in the report, but the woman said she had recently read an article about him, "full of praise."
Francois Polet, another employee at Cetri, said the organization decided not to go public with the reason for Houtart's resignation from the board at the victim's sister's request. He said the precise relationship between the Houtart and the victim -- whether he was a cousin, nephew, or more distant relative -- wasn't clear.
"It was a big, big surprise and a big, big (disappointment)," Polet said of the revelation. "Directly for us it was very clear that we could not continue to have some kind of collaboration" with Houtart.