In November last year, a newborn boy in Brooklyn was brought to his pediatrician’s office because he was being unusually fussy after feedings. The doctor discovered a cluster of lesions on the boy’s penis, then learned that during the boy’s recent circumcision ceremony, the circumciser who performed it had used his mouth to suck blood away from the incision.

Like three other babies last year, the boy had a potentially fatal herpes infection following an ancient Jewish ritual known as metzitzah b’peh, or oral suction. The administration of Mayor Michael R. Bloomberg had tried to regulate the practice , over the fierce objections of ultra-Orthodox rabbis, by requiring that the circumcisers have parents sign a consent form that acknowledged their awareness of the procedure’s risks.

More than two years after the regulation was passed, however, the consent forms appear to be rarely used. Meanwhile, the number of herpes infections suspected to have been caused by the practice in New York City jumped last year.

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The situation now presents a conundrum for Mayor Bill de Blasio . City health officials have advised that the ritual should never be performed, but the growing ultra-Orthodox Jewish community that cherishes it represents a crucial political constituency for Mr. de Blasio. So he pledged during his campaign to rescind the consent requirement on “Day 1” of his administration and find a solution that would be more acceptable to Orthodox leaders, while still protecting children’s health.

Members of the de Blasio administration have conferred about half a dozen times over the last year with Orthodox leaders about the issue and are now close to a compromise agreement, said Avi Fink, the mayor’s deputy director of intergovernmental affairs, an Orthodox Jew involved in the discussions. The goal of the new rule would be to better educate parents about the ritual’s health risks, while respecting their right to have it done, he said.

“You can have something on paper that seems robust, and maybe even seems invasive and strong,” Mr. Fink said of the consent requirement. “But part of how the mayor is going to ensure success in this is how many people are we actually touching and communicating with, and how much awareness and education can we actually accomplish.”

Metzitzah b’peh is a regular part of the circumcision ceremony within some branches of Orthodox and ultra-Orthodox Judaism, but is rare among other Jews. In 2012, a report by the Centers for Disease Control and Prevention estimated that it was conducted on about 3,600 New York City newborns each year. The researchers advised against the practice, warning that it raises the likelihood that an infant will get herpes by 3.4 times that of other male newborns.

In September 2012, city health officials mandated that every Jewish ritual circumciser, known as a mohel, collect consent forms. The form must state that the city advises against oral suction because it “exposes an infant to the risk of transmission of herpes simplex virus infection, which may result in brain damage or death.” Mohelim should retain the signed forms for a year, in case of an investigation.

Soon after the rule’s passage, more than 200 ultra-Orthodox rabbis ordered their followers not to comply. Orthodox leaders also sued the city in federal court, arguing the regulation was unconstitutional. While a district court sided with the city, an appeals court in August expressed concern that the rule could indeed curtail freedom of religion. Its judges directed the lower court to start over, using a stricter legal standard.

Through the legal wrangling, the regulation has remained in effect, though apparently seldom followed. A. Romi Cohn, an Orthodox Jew who is the head of the American Board of Ritual Circumcision and estimates he has conducted about 25,000 circumcisions in his lifetime, said he had never used the consent form. He added that he did not believe the roughly 80 other mohelim affiliated with the association had either.

Mr. Cohn, 85, says he believes that when properly conducted according to the God-given tradition, the ritual is safe. His association mandates annual herpes testing and other precautions, like having mohelim rinse with antiseptic mouthwash before the ritual.

“We do it because Hashem commands us, and because it’s healthy and necessary,” he said, using a Hebrew word referring to God, after conducting a bris, or circumcision ceremony, last month at a synagogue in Midwood, Brooklyn. “Whenever God tells us to do something, it is to our benefit.”

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The newborn that Mr. Cohn circumcised that morning, Yeoshua Setareh, was the third boy in the family whom he had circumcised. The father, Bijan Setareh, is a dermatologist.

“If our rabbi says do it, we do it with a closed eye,” Dr. Setareh said of why he approved of the ritual. Limor Setareh, his wife, said, “We believe that it’s a divine thing, and if it’s a divine thing, it doesn’t change with time.”

Mr. Cohn does give out a consent form warning that circumcision, like any medical procedure, has risks, but it does not mention oral suction. Rabbi Shimon Hess, another well-known ultra-Orthodox mohel, said he drew up his own form in response to the Bloomberg regulation. It stated, he said: “I am knowledgeable that New York City says metzitzah b’peh is dangerous. However, I trust the Talmud, and that the Talmud says that not to do metzitzah b’peh is dangerous.”

The health department has never tried to collect consent forms en masse. Enforcement, it said when the regulation passed, would be only in the case of a complaint or a suspected case of herpes.

“Its self-enforcement essentially,” said Sam Miller, a spokesman for the department. “We are not going around to brises.”

The city has not had much success in curbing infections. In 2014, there were four infections judged to be linked to oral suction, double the number in 2013. Between 2000 and 2012, there were 11 cases in all, with two being the greatest number in a single year.

Among the six herpes cases following oral suction since 2012, parents were willing to identify the mohelim in only two cases. One of those mohelim produced a consent form; the other did not. Both were barred from conducting oral suction, because both refused to be tested for the virus. But health officials have no way of knowing if they are adhering to the ban, unless someone reports them.

Suburban Rockland County, also home to many ultra-Orthodox Jews, worked with rabbis two years ago to create a voluntary protocol that has successfully tested mohelim and others who came in contact with an infected newborn, as reported recently in Capital New York. No cases of transmission through oral suction have been proven, said Dr. Oscar Alleyne, the county’s director of epidemiology.

De Blasio administration officials are hoping their regulation will be more effective than the Bloomberg administration’s rule in reducing the infection rate, contending that at least some Orthodox rabbis agreed that government had a role to play in educating on the issue.

But because of the extreme sensitivities among the ultra-Orthodox about any interference with the rite of circumcision, there will be limits on what kind of consensus is possible.

“We feel very strongly that the goal ought to be, ‘Let’s get rid of any formal, governmental regulation,’?” said Rabbi David Zwiebel, executive director of Agudath Israel, a powerful ultra-Orthodox umbrella group that is among those suing over the consent requirement, and whose cooperation would be crucial to a new rule’s success. “Once you acknowledge this is subject to governmental regulation, then you have taken the first step in a journey which could easily lead to an outright ban of the practice, which is a scary thought.”