There was a sense of relief at nine low-performing city high schools on Thursday as the city’s Department of Education announced they would not be closed next year. The decisions came after months of uncertainty about the schools’ future.

But with the relief came concern and confusion over what exactly would happen to the schools, which instead will go through a federal process known as the restart model, which has not been tried before in New York City.

“I am pleased that they have come to a decision not to close the school,” said Dominick Scarola, the principal of Grover Cleveland High School in Queens, one of the nine, “but I am still a bit apprehensive because I am not sure how it is going to roll out.”

Each of the nine schools is eligible to receive up to $6 million over three years to transform its lower-than-average graduation rate into an educational success story. But to qualify for the money, the city has to contract with outside organizations to see if they can do a better job managing the school than the city did.

That raises a host of questions about how much authority these organizations, nonprofit groups that will be called educational partnership organizations, will have to lead the schools.

Principals were told on Thursday that there would be no staff or leadership changes “at this time” — and parents were told in a letter that all the children would remain in place — as the administration and the educational partnership organization “work together to determine how to strengthen the curriculum, develop academic supports for students, and help teachers improve practice.”

The city has not chosen the partner groups, but they would most likely be management companies like New Visions for Public Schools, Urban Assembly and Generation Schools, which already work in the school system.

One principal, speaking on the condition of anonymity because he did not want to criticize a program that would be working with his school, said, “Restart is the wrong word, because they are not changing anything.”

But according to state law, the new organizations will have the power to make recommendations about the hiring and dismissal of principals and teachers, just as a district superintendent would. They will answer to the chancellor, who will make the final decisions. That sets up a potentially fraught situation in schools receiving support.

The city is due to make decisions about 31 other low-achieving schools on Friday. They will either join the restart program, or forgo the federal money. There are two other possible blueprints for the grant, but they require agreement from the teachers’ union, and negotiations have stalled over how teachers would be evaluated within them.

The schools that were announced on Thursday for restart include Herbert H. Lehman High School in the Bronx; John Dewey High School in Brooklyn; and Richmond Hill High School, John Adams High School and Newtown High School in Queens.

Michael Mulgrew, the president of the teachers’ union, said he was pleased that the schools would be improved and not closed, and said he understood that the partner organization “runs the school.”

“We are looking forward to working with some of these partners,” he said. “They have to come up with an educational plan and actually support it, and this is something that the Department of Education has not been able to do.”