A running legal battle between Orleans Parish Clerk of Criminal Court Arthur Morrell and Mayor Mitch Landrieu’s administration is headed back to a civil court judge to decide just how much, if anything, the city owes Morrell for withholding some funding for his office in recent years.

According to Morrell, the running total is closing in on $3 million. The city’s estimate: zero.

A panel of the state 4th Circuit Court of Appeal found Wednesday that while Civil District Court Judge Sidney Cates IV ruled in Morrell’s favor last year, saying that the city must fully fund the court clerk’s staff under state law, the judge never decided whether the city broke the law or how much it owed.

Some cuts to Morrell’s budget are allowed, the appeals court ruled, so long as the city meets the mandates of a state law requiring it to fully fund Morrell’s staff.

Morrell sued the city in 2012, accusing Chief Administrative Officer Andy Kopplin of illegally holding back funds from his office, first temporarily and then as a permanent reduction.

Kopplin has long claimed that Morrell has repeatedly overspent his budget and that the city has the right to require him to keep a lid on his spending. Morrell argues that the administration has no right to refuse to pay the full tab for his budgeted staff of 901/2 employees.

Morrell said Thursday that a de facto hiring freeze by the city has left him with 23 vacant positions.

“I haven’t filled a position since October 2012,” he said. “I can hire them. They just won’t pay for them.”

Blaming the city, Morrell said he was forced recently to halt overnight bail bond processing from 11 p.m. to 7 a.m., meaning people seeking to bail someone out of Orleans Parish Prison must wait until morning.

He also has sharply curtailed staffing of the evidence room. He said he would shutter the room an additional day starting Monday, allowing prosecutors and attorneys to view evidence only by appointment on Tuesdays, Wednesdays and Thursdays.

Morrell said he notified the criminal court judges and District Attorney Leon Cannizzaro of the move, which threatens to further slow the pace of criminal cases at the courthouse at Tulane Avenue and Broad Street.

State law mandates that the city pay for the salaries of Morrell’s deputy clerks. After Morrell sued the city, the Legislature passed another law that clarified that requirement and mandated that the city first seek legislative approval before cutting “expenses, including salaries and maintenance of constitutional officers, their deputies, subordinates and employees” in the office.

Morrell’s lawsuit covers only the city’s alleged failure to pay all the money it owed him for 2012 ­— an amount Morrell pegged at a few hundred thousand dollars. But he argues that the city also should be forced to pay the full funding difference since then. The money Morrell claims the city is shorting him — about $1 million this year — is needed to play catch-up, he said.

“We’ve got scanning, filing, stocking that have been put on the back (burner), just so we can operate the court,” he said.

Morrell estimates that the city owes him $2.7 million, spokeswoman Danae Columbus said Thursday.

Mayoral spokeswoman Garnesha Crawford said in a statement that the appeals court agreed the city “has the legal right to set funding levels for (Morrell’s office) at a discretionary amount. Furthermore, we are confident the evidence will prove the city has met all legal obligations in this matter.”

Follow John Simerman on Twitter, @johnsimerman.