The apology appears in Friday's editions of Boston archdiocese newspaper.
O'Malley became Boston's archbishop about nine months ago, after a series of clergy sex-abuse scandals and alleged church cover-ups led to the resignation of Cardinal Bernard Law.
The new archbishop did not include women, as Law often did, in the Holy Thursday ritual foot-washing, an act showing the humility of the priest. According to the Boston Globe, O'Malley in an April 6 sermon said baby boomers are "heirs to Woodstock, the drug culture, the sexual revolution, feminism, the breakdown of authority and divorce."
Catholic women had complained to parish priests of the two events.
O'Malley wrote, "Other influences I mentioned were obviously negative, and so my comment was construed as an attack on feminism." He also said he "values the gifts and contributions that women make to our church and to my own faith life."
O'Malley wrote that being archbishop of Boston is "like living in a fishbowl made out of magnifying glass." He added, however, that "some people seem determined to make our liturgical services a political battleground."