The national debate over giving schoolgirls a vaccine that can help prevent cervical cancer is coming to the fore at a public high school in Manhattan, where a health center was administering the vaccine until school officials asked for a temporary halt.

The school-based health center at Washington Irving High School, on Irving Place near Union Square, began administering the vaccine for human papillomavirus several weeks ago, officials at the clinic said, and so far has treated about a dozen girls.

Religious and politically conservative groups nationwide have worried that offering the vaccine will encourage girls to have sex. The governor of Texas, J. Richard Perry, a Republican, recently mandated the vaccine for 11- and 12-year-old girls, saying he did not want them to get cervical cancer. But some critics from the medical community expressed concern over the vaccine’s long-term effects. As more states consider legislation mandating the vaccine, including New York, some have also criticized the advertising and lobbying efforts of the vaccine’s manufacturer, Merck.

“From a public health perspective, when you’re dealing with teens who have a lot of health risks, sexually transmitted infections being one of them, you feel it’s your responsibility to inform them of this choice,” said Dr. Robert Schiller, the senior vice president for clinical services at the Institute for Urban Family Health, which operates the clinic at Washington Irving High School.

Dr. Schiller said the health center is temporarily on a “time-out,” after it agreed to allow a pause to clarify the role of the Department of Education, the school’s principal, and parents. The line is somewhat murky because although the health center is inside the school, it is independent from the Department of Education. It receives funding and partial oversight from the state’s Department of Health.

This week, Dr. Schiller said doctors at the health center initially introduced Gardasil like they would any other vaccine, and received payment for it from Medicaid and private insurance plans, as well as from the city for those students whose financial needs made them eligible. The groundswell of contention over the vaccine reached the school just as doctors began administering the drug, which costs $360 for a three-part dose administered by injections in the arm.

He said, “This is not like giving out other vaccines, and I think that’s been obvious.”

The result of the national debate and the press attention that went along with it has been that in New York City doctors reported an increase in the number of women interested in the vaccine. That group apparently included high school students at Washington Irving.

A spokeswoman for the Department of Education, Margie Feinberg, explained the “time out” by saying that before introducing changes in procedure, clinic representatives typically speak to the school’s principal and parents. “That’s all we are asking of them now,” she said.

The Department of Education yesterday sent a letter to principals of schools that house independent health centers, encouraging the clinics to offer Gardasil to female students. “We have also encouraged providers to discuss this vaccine with parents before starting to administer it,” the letter read.

Reached after the letter had been sent, Dr. Schiller said the clinic respects the Department of Education process, and would work with the school to reinstate vaccinations, hopefully within a week. “We’re just trying to do the right thing,” he said.

Gardasil protects against four strains of the HPV, including two linked with 70% of cervical cancer cases. In June, it received FDA approval for women ages 9 to 26. The Centers for Disease Control and Prevention later recommended it for 11- and 12-year-olds.

Many doctors support the vaccination. “It is very effective in protecting against the two most common high-risk types of the human papilloma virus, which lead to severe dysplasia and cancers,” a gynecological oncologist in Manhattan, Dr. Elizabeth Poynor, said.

Still, the vaccine has critics, particularly among those who oppose mandatory vaccination. “With 11 and 12-year-old girls, you are talking about girls five years off their tricycles and now they are being engineered for sexually transmitted diseases,” a spokeswoman for the Catholic League for Religious and Civil Rights, Kiera McCaffrey, said. She drew a distinction, however, with Washington Irving’s opt-in process.

Among students there, many interviewed said they want to be vaccinated. “I think it’s a good idea because it’s going to help us girls not get cervical cancer,” a 16-year-old student who identified herself as Paula, but declined to give her last name, said.

One 12th grader rejected the idea that vaccinating young women would encourage them to have sex. “There’s still AIDS and HIV and other STDs,” the 17-year-old student, Kimberly, said.

The mother of a 16-year-old public school student also supported the initiative. “I do think by offering the service, it’s terrific,” Bijou Miller, who is co-secretary of the District 2 Parent’s Council, said. Her daughter recently was vaccinated because, she said, “If there’s one kind of cancer I can help prevent her from getting, why not?”

City and state policy makers have said they support the vaccine.

“Studies show that the vaccine will provide the best possible protection against cervical cancer,” a spokesman for the state’s health department, Jeffrey Hammond, said. “Rarely does an opportunity come along to prevent a cancer this effectively to help protect children.”