A disagreement about who should control the purse strings as Fulton County embarks on a criminal justice reform plan could send the county jail back to the bad old days of federal court oversight.

The tension between Fulton County commissioners and judges and other court officials about how an overhaul of the justice system should be funded might cost jobs and stop a program that assesses every one of the 26,000 inmates booked into the jail each year.

A scheduled end to the pretrial services program on April 5 could result in jail overcrowding that would lead to lawsuits, warned Sara Totonchi, executive director of the Southern Center for Human Rights. The county jail just last year was released from more than a decade of oversight that stemmed from a lawsuit her organization filed.

That suit, which cost the county about $1 billion in renovations and repairs, began in 2004 when an inmate complained about conditions at the jail. The issues — including faulty locks that let inmates wander, raw sewage that flooded cells and overcrowding that was so bad that inmates slept on the floor — were so egregious that oversight lasted five times longer than it has in similar cases, the judge said in lifting the order.

Reforming the justice system has been of paramount importance to John Eaves, chairman of the Fulton County Board of Commissioners. He proposed the county take $10 million from judicial budgets to reinvest in solving the problems, but capitulated when the courts and others said such a loss of funds would hamstring them.

A compromise was reached at $5 million, but now, everyone from the public defender to the chief judge of superior court is fighting to regain access to that withheld money. On Monday, Eaves plans to present an agreement that would return the remaining $5 million.

“They have the feeling we are not granting them as much autonomy in the whole process,” Eaves said. “There’s going to be some tension as change comes about.”

If the funds are redistributed, Chief Judge Gail Tusan told commissioners, her team will continue to work toward fixing the overarching issues with the justice system. But to withhold that money now puts effective programs at risk.

“Timing is important,” she said. “This was to try to keep everyone in discussions, to relieve the stress from the hold-back.”

An end to pre-trial services, which include interviews of those who are arrested to determine demographic and income information that helps with bond motions, would delay the judicial process, said Vernon J. Pitts Jr., public defender of the Atlanta Judicial Circuit.

“It’s going to slow the system down and increase the jail population,” Pitts said. “There would be a substantial delay getting people out of jail, people who should be out of jail.”

In a letter to commissioners and others sent earlier this month, Totonchi said the existing county model has reduced jail overcrowding, but cuts to the system designed to free money up for an overhaul could threaten it again.

“It would be truly unfortunate to see so much hard work undone by ill-conceived budget cuts and program elimination,” she wrote.

Eaves wants to reduce the jail population, as well as improve mental health services that would keep people out of the jail entirely.

Over the past several months, commissioners have approved hundreds of thousands of dollars worth of contracts to study the system and provide recommendations for an overhaul. Eaves said despite money-related protestations, he is “undeterred” in his goal to change the system.

By the end of April, Eaves said, he expects to have signed a memorandum of understanding with judicial partners that would reinstate the $5 million that was going to be spent on reform. In exchange, he will get a “gentleman’s agreement” that they will work together to find solutions.

Returning the money, though, means it will likely be another year before any substantial changes are made. Eaves had hoped to have something in the works over the summer.

“There may be some turbulence, but that doesn’t mean we won’t get to the destination,” he said. “It’s complicated, but it’s exciting to me. When we get to the promised land, it will be a great day for the county.”