A program at CUNY aimed at recruiting and retaining black male students is coming under the scrutiny of federal anti-discrimination investigators.

The federal Department of Education recently opened an inquiry into the program’s presence on 16 CUNY campuses, including Baruch, Brooklyn, and John Jay colleges, according to a letter from the education department’s office for civil rights.

The program, known as the Black Male Initiative, was launched across the university system in 2005 and receives annual funding of between $1.5 million and $2.5 million from the City Council. Different colleges within CUNY have undertaken a range of programs as part of the initiative. The Bronx Community College is establishing a tutoring service to assist “at risk” students, according to CUNY’s Web site. The Graduate School and University Center sponsor recruitment visits from out-of-town applicants who belong to the “target population.

Of interest to the federal Department of Education is whether these or other programs of the Black Male Initiative violate federal laws prohibiting race or gender discrimination. Last week, the agency sent a letter outlining the investigation to the director of the New York Civil Rights Coalition, Michael Meyers, who had filed a formal complaint about the program in 2006. “This indicates that CUNY is in trouble, for the Office of Civil Rights to open up investigations under their own steam, on all the programs they could,” Mr. Meyers said. “These programs are discriminatory against black men by segregating them and stigmatizing them.”

It is unclear whether any CUNY students have complained about the program to the federal Department of Education or to the state or city agencies whose task it is to enforce various anti-discrimination laws.

A university spokesman, Michael Arena, wrote in an e-mail message that programs of the Black Male Initiative are “open to all academically eligible students” regardless of race or gender.

Within the university, the Black Male Initiative began at Medgar Evers College, where most of the students are black women. The college created the Male Development and Empowerment Center in 2004.

In 2005, the university chancellor, Matthew Goldstein, expanded the initiative across the CUNY system. A university task force commissioned by Mr. Goldstein has made recommendations on topics ranging from how to reduce incarceration rates for black men and how to increase employment opportunities for black men.

Programs similar to the initiative exist in a handful of public universities across the country, but Mr. Meyers said he believes CUNY’s was the first to receive scrutiny from civil rights investigators at the federal Department of Education.

The chairman of the council’s Committee for Higher Education, Charles Barron, said the investigation was “a waste of taxpayer money” and a “witch hunt.”

“Money is earmarked for woman’s programs or Asian studies — ethnic-specific funding goes on all the time,” he said.