New York City will soon assemble an army of more than 1,000 disease detectives to trace the contacts of every person who tests positive for the coronavirus, an approach seen as crucial to quelling the outbreak and paving the way to reopen the hobbled city.

But that effort will not be led by the city’s renowned Health Department, which for decades has conducted contact tracing for diseases such as tuberculosis, H.I.V. and Ebola, city officials said on Thursday.

Instead, in a sharp departure from current and past practice, the city is going to put the vast new public health apparatus in the hands of its public hospital system, Health and Hospitals, city officials acknowledged after being approached by The New York Times about the changes.

The decision, which Mayor Bill de Blasio is preparing to announce as early as Friday, puzzled current and former health officials, who questioned the wisdom of changing what has worked before, especially during a pandemic.

The department conducted tracing of coronavirus cases at the start of the outbreak, and had been doing so again recently, in preparation for the city’s expansion.

Dr. Mary T. Bassett, a former city health commissioner under Mr. de Blasio and now the director of the FXB Center for Health and Human Rights at Harvard University, said that the three key elements of handling the coronavirus — testing, tracing and quarantine — have long been performed by the Health Department.

“These are core functions of public health agencies around the world, including New York City, which has decades of experience,” Dr. Bassett said in an email. “To confront Covid-19, it makes sense to build on this expertise.”

The move also angered some within the ranks of the Health Department, which has been at odds with Mr. de Blasio since the early days of the outbreak, when top officials in the department clashed with City Hall over the timing of school closures and public health messaging.

Dr. Mitchell Katz, the head of Health and Hospitals, said that the move was made because his agency, a public benefit corporation rather than a city department, could more quickly hire contact tracers and enter into contracts for testing and other needed services.

His agency, he said, would also oversee the hotels for housing people who could not quarantine at home, as well as some coronavirus testing.

But he said the tracing itself would be supervised by a team of roughly 50 Health Department experts who will be detailed to Health and Hospitals to run the operation.

“So we’ll be able to have the best of both worlds,” he said. “We’ll be able to have the people who are used to supervising this kind of work still doing the supervision of it. But we’ll be able to hire as quickly as possible and get as many tests done” as possible.

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Credit…Gabriela Bhaskar for The New York Times

The city’s public hospital system struggled with budgetary shortfalls even before the coronavirus outbreak sent thousands of sick and dying patients into its 11 hospitals. Their emergency rooms have been the front lines of the crisis, as doctors and nurses faced a wave of patients at facilities including Elmhurst Hospital in Queens and Woodhull Hospital in Brooklyn. Staff members died, even some who did not work directly with patients.

A spokeswoman for Mr. de Blasio declined to comment about any dissatisfaction expressed by Health Department officials and declined to make the city health commissioner, Dr. Oxiris Barbot, available to discuss the matter.

Contact tracing is one part of an accepted strategy for responding to disease outbreaks, and it is now at the center of a national discussion of how and when to begin allowing economic activity to restart. State officials included the number of contact tracers working in a region as one key metric for determining when businesses in that region would able to reopen.

Mr. de Blasio, in recent days, has talked repeatedly about the large new public health system that will be needed to contain the virus as the number of new cases recedes. Officials have said the efforts are essential to reviving the city’s economic life.

“You’re talking about tens of thousands of people who will be tested daily,” the mayor said in an interview on MSNBC on Sunday. “You’re talking about a tracing apparatus that, anyone who is tested positive, we ask them, we interview them: who they’ve been close with in recent days, who they’ve come in contact with.”

Before the shift, hiring was being conducted by the nonprofit Fund for Public Health in New York City in partnership with the Health Department; salaries for contact tracers started at $57,000 a year. Thousands had already applied.

Dr. Thomas R. Frieden, the former director of the Centers for Disease Control and Prevention and former New York City health commissioner, said that the city’s Health Department is the “greatest in the world” and that “if any health department can excel at contact tracing, New York City can.”

David Harvey, executive director of the National Coalition of STD Directors, a membership organization of health officials who deal with contact tracing to limit the spread of sexually transmitted diseases, said that while there was a “role for the health care delivery system to coordinate with the health department,” the group was concerned that the mayor’s decision might slow the implementation of contract tracing in the city.

“New York is leading the nation as the epicenter of this epidemic and it is a leader of the nation,” Mr. Harvey added. “We are worried about anything that delays the rollout of an expanded contact tracing program.”

The Health Department has the authority to issue quarantine orders in New York City. Such orders are likely to be an important part of the program, which would not only involve getting in touch with people who have had close contact with an infected person, but also getting those contacts to quarantine themselves, either at home or, possibly, in a city-funded hotel.

During the Ebola outbreak early in Mr. de Blasio’s first term, the Health Department created a telephone center to track potential contacts.

As the rapid spread of infections overwhelmed the system in late March and April, the city largely stopped doing contact tracing on confirmed Covid-19 cases. In recent weeks, health workers have been doing a few case investigations to prepare to ramp up the system, and they plan to restart tracing on a broad scale once hundreds of new people have been hired.

Yet the city has never tried to trace a disease as commonplace in the population as Covid-19, Dr. Shama Ahuja, who oversees tuberculosis contact tracing for the Health Department, said in an interview last week.

“It is like tracing the flu,” she said. “The level of this effort is unprecedented.”

Sharon Otterman contributed reporting.