San Francisco Superior Court, faced with a deficit of nearly $5.3 million, says it will close its clerks’ offices at 1 p.m. on Fridays and require court staff to take Fridays off on a rotating basis, without pay.

The closures will start in September and continue through June, Presiding Judge Teri Jackson said Monday. The unpaid furloughs will begin Aug. 4.

The deficit arose from a 9 percent cut in state funding for the fiscal year that started July 1, Jackson said. She said four unions representing the workers had accepted the furloughs, which will require each staffer to miss one Friday per month through next June, to avoid layoffs.

The court is considering other money-saving measures, including a freeze on hiring, Jackson said.

“We are committed to keeping our courtrooms open and continuing to prioritize access to justice” despite the reductions, Jackson said in a statement.

With clerks’ offices closing earlier on Fridays, drop boxes will be available outside each office from 1 to 4 p.m. for documents that will be file-stamped on that day, the court said.

The state budget approved by Gov. Jerry Brown and the Legislature for the new fiscal year includes about $3.7 billion for the judiciary, about the same as last year, despite the contention of California Chief Justice Tani Cantil-Sakauye that trial courts badly needed more funding after years of cuts. The state provides a large majority of the courts’ funding, and local fees cover most of the rest.

The San Francisco court’s funding declined because of rules adopted by the state courts’ Judicial Council in 2013 that allocate an increasing share of state dollars to courts with relatively higher workloads for their judges.

Jackson said the San Francisco court suffered a 9 percent cut, the largest of any county, reducing its state funding to $51.7 million. In 2008, before the recession, the court had a $90.5 million budget and nearly 600 nonjudicial employees, compared with about 430 now, Jackson said. The court started laying off employees in 2011 after the first round of state budget cuts.

The court’s judges will not be furloughed, but Jackson said they had agreed to make voluntary contributions to help support court operations. She said she was requesting an amount equal to one day of their pay per month, about $509, from Aug. 1 through June.

The clerks’ offices are at the court’s headquarters at 400 McAllister St., the criminal and traffic courts at 850 Bryant St., and the Juvenile Justice Center at 375 Woodside Ave.

Bob Egelko is a San Francisco Chronicle staff writer. Email: begelko@sfchronicle.com Twitter: @egelko