There have been many moments of greatness over the decades for the Boys Choir of Harlem – concerts around the world, audiences including Nelson Mandela and Pope John Paul II. But the choir has also struggled in recent years with financial troubles, and management issues in the wake of a sexual abuse scandal.

Now, with the organization up to $5 million in debt, the choir is facing the loss of its home as well.

The city has told the Boys Choir to leave the public school where it has operated rent-free since 1993. Citing concern about the group’s financial and management difficulties, the Department of Education sent a letter last month saying the choir must vacate its office space by January 31.

The children may still be able to use the building for after-school rehearsal. But as a partner in the school itself, city officials say the choir’s administration isn’t living up to its responsibilities.

Boys Choir supporters, including Mayor Dinkins and Rep. Charles Rangel, are asking the city to reconsider, or at least give it until the end of the school year to move. They have been meeting with city officials, and made a presentation for a plan to improve the situation.

“We have in hand pledges, commitments exceeding a million dollars, and more forthcoming, but that will only be so if it appears that the city is willing to continue this partnership which has been so successful,” Mr. Dinkins said.

The city isn’t backing down.

The deputy mayor, Dennis Walcott, said the education department’s top priority is its responsibility to the more than 600 students in the school, I.S./H.S. M469, otherwise known as the Choir Academy of Harlem.

The city hires the school’s teachers and provides equipment and standard academic curriculum, while the choir organization is responsible for funding counselors, tutors, musical training, and a mandatory summer institute.

But the education department said in its letter that the choir staff had stopped showing up for music and counseling duties, seemingly because the staff was not being paid. The department said it even had problems getting reliable information about the choir’s touring dates, which affect attendance by students performing in the choir.

Fewer than 125 of the school’s students perform in the Boys Choir of Harlem and the organization’s newer girls choir. The department estimates the value of the use of the facilities by the choir organization at $550,000 a year.

The choir “is using the school for free administrative and rehearsal space but is not providing students with the instruction and services that were the basis for our partnership,” the education department letter said.