The 83-year-old Buddhist monk from Tibet, who has been in and out of the hospital recently, doubled down on a sexist comment he made in 2015.
His Holiness told the BBC: "If a female Dalai Lama comes, she should be more attractive."
But in a "clarification" his office released on Tuesday, he apologized.
"In responding to a question about whether his own reincarnation could be a woman, and suggesting that if she were she should be attractive, His Holiness genuinely meant no [offense]," the statement read. "He is deeply sorry that people have been hurt by what he said and offers his sincere apologies."
While he explained further that in Buddhism outward and inward beauty matter, the office of the Dalai Lama explains, "His Holiness consistently emphasizes the need for people to connect with each other on a deeper human level, rather than getting caught up in preconceptions based on superficial appearances."
The issue dates back to 1992 when the Paris editor of Vogue magazine asked him if a future Dalai Lama could be a woman, according to the office.
The statement seemed to suggest the monk made the comments in jest.
"His Holiness, a monk now in his mid-80s, has a keen sense of the contradictions between the materialistic, globalized world he encounters on his travels and the complex, more esoteric ideas about reincarnation that are at the heart of Tibetan Buddhist tradition. However, it sometimes happens that off the cuff remarks, which might be amusing in one cultural context, lose their humour in translation when brought into another."
The statement did not apologize for remarks he made about President Trump for his "lack of moral character."