The site — 4parents.gov — stresses the promotion of abstinence.
Emphasizing abstinence is fine, said the groups, but the government also should stress the need for contraception if sexual relations do occur.
"There's this misconception that giving young people negative information about contraception will encourage them not to have sexual intercourse, when all it will do is encourage them not to have contraception, so the strategy backfires," Monica Rodriguez, an official at the Sexuality Information and Education Council of the United States, said Thursday.
The council, which also provides sex education materials, sent a letter addressing its concerns to Michael Leavitt, secretary of the Health and Human Services Department. More than 100 organizations, primarily liberal advocacy groups, signed on, including the American Civil Liberties Union, the Human Rights Campaign and Planned Parenthood.
Leavitt said in a statement unveiling the site last week that it was designed for parents who are embarrassed about talking with their children about sex.
"Parents have a tremendous amount of influence on their children and we want them to talk with their teens about abstinence so that they can stay safe and healthy," he said.
HHS officials said Thursday evening they were not surprised certain groups disliked the site.
"They've always opposed us on the issue of abstinence. That's fine," HHS spokesman Bill Pierce said. "One thing we do know about abstinence is that if you practice it, you will not have an unintended pregnancy or risk catching a sexually transmitted disease."
The site advises parents to tell their teens why they should not have sex: "Tell them abstinence is the healthiest choice. They will not have to worry about getting pregnant or getting someone pregnant. They will not have to worry about sexually transmitted diseases, including HIV/AIDS. Nor will they have to worry that the person they are dating is only interested in them because of sex."
The Human Rights Campaign said it was particularly concerned about sections of the Web site that focus on sexual orientation. The group works for equal rights for gays, lesbians and bisexuals.
The site says: "If you believe your adolescent may be gay, or is experiencing difficulties with gender identity or sexual orientation issues, consider seeing a family therapist who shares your values to clarify and work through these issues."
Joe Solmonese, president of the Human Rights Campaign, said in a separate letter to Leavitt, that describing sexual orientation as an "alternative lifestyle" is outdated and inaccurate language that can alienate youth at a time when they are particularly vulnerable.
"By terming sexual orientation a 'lifestyle,' HHS is discussing it as a matter of choice, which is contrary to the vast majority of scientific evidence. Sexual orientation is not a lifestyle," Solmonese said.
The site describes condoms as imperfect, saying they can break or be used incorrectly, and it includes a chart of whether a condom protects a little, some, or a lot, against various sexually transmitted diseases.
Patrick Fagan, a research fellow at the Heritage Foundation, a conservative think tank, said the Web site's information about condoms looked accurate.
"This is standard, straightforward research on the effectiveness of condoms," he said.
Fagan also said the Web site would be useful for parents of gays and lesbians. He said they deserved to get the same information made available to parents of heterosexual children.
"Teenagers involved in homosexual acts ... are worth the same transmission of information on the effectiveness of condoms and on the dangers of sexually transmitted diseases," he said.