New Yorkers are becoming infected with HIV at three times the national rate, according to new data from the city’s Department of Health and Mental Hygiene.

Based on a new model for tracking recent infections developed by the Centers for Disease Control, city health officials estimated that 72 out of every 100,000 New Yorkers contracted the virus that causes AIDS in 2006, compared with 23 out of every 100,000 individuals in America. Overall, 4,800 New Yorkers became infected with HIV that year, including 3,863 New York City residents.

The CDC’s new model uses a technology to analyze blood samples to determine if an HIV infection is recent or has been ongoing. Earlier this month, CDC officials said the number of new HIV infections each year is 40% higher than they previously thought. They reported that 56,400 people became infected with HIV in 2006, a revision of their earlier estimate that 40,000 Americans become infected with HIV each year.

In New York City, widely considered an epicenter of the HIV and AIDS epidemic, more than 100,000 are infected with HIV, according to the health department. Officials cited demographics to explain the disparity in infection rates, saying large segments of at-risk populations live in the city. They further said the new incidence rate would influence where they target their prevention efforts.

“We have a lot of work to do and we’re continuing to do it,” the health department’s assistant commissioner for HIV/AIDS prevention and control, Dr. Monica Sweeney, said. She cited the city’s campaign to distribute free condoms, and said officials were looking to increase that effort. Last year, the city gave away 38 million free condoms, and health officials said they are on track to exceed that number this year.

According to the department’s calculations, 50% of the new infections — about 2,372 cases — occurred among men who had sex with other men, while 8%, or 372, came from intravenous drug use. The vast majority of cases occurred among men, who accounted for 76% of infections in 2006. Nearly half of the new infections, 46%, occurred among black New Yorkers, while those between the ages of 30 and 39 accounted for 29% of the new infections.

“That’s distressing,” a professor of applied psychology and public health at New York University, Perry Halkitis, said. “It says to me that somewhere along the line, we didn’t fully address the needs of this group of young men.”

Mr. Halkitis, who is working with the health department to develop new prevention messages for young gay men, raised a concern echoed by others that the health department’s condom campaign may be too simplistic. “‘Use a condom every time,’ while it sounds like a good message, it’s not an effective message,” he said.

Some HIV/AIDS groups that support the city’s condom campaign also said city health officials should go further.

“These prevention problems have to go another step deeper into the underlying factors in prevention and treatment,” the managing director of social responsibility at the Gay Men’s Health Crisis, Samantha Taylor, said. “The condom distribution program is excellent, but there are still a lot of people out there who don’t know what to do with them.”

Ms. Taylor said she was particularly concerned because Mayor Bloomberg and the City Council earlier this year approved a $5 million cut to HIV/AIDS programs and services.

Some criticized the health department’s tactics altogether, and in particular the campaign to distribute free condoms.

“When you promiscuously distribute it on the street corners, as if it were a lollipop, you’re sending a message, however unwittingly, that this is kind of casual,” the president of the Catholic League for Religious and Civil Rights, Bill Donohue, said.