Chief Justice nominee Tani Cantil-Sakauye chaired the committee recommending the pay hike for the Judicial Council's staff, which is called the Administrative Office of the Courts.
The 3.5 percent raise will go to most of its 800 employees.
Cantil-Sakauye says belt tightening measures over several years makes it all this possible.
"The money that was saved through basically employee effort and employee sacrifices now is available," Cantil-Sakauye said.
Employees of the state's 58 local county courts are not covered by the pay raises. They want the money to be used to improve the courts which have been hit hard by the state budget crisis.
"It feels like a slap in the face for us because basically it feels they're saying to us, 'We're not concerned about the services you're providing to the public,'" William Trupek of the SEUI for San Francisco courts said.
Judges Tia Fischer and David Lampe are with the Alliance of California Judges, a group that wants to reform the judiciary. They wonder how the public will react to a pay raise.
"The workers who've lost their health insurance? Not well. The public court employees who were laid off? Not well," Fischer said.
Council members pushing for the raise say it is simply restoring salary reductions that Judicial Council staff took over the years.
"The first thing to recognize is this is not a pay raise," Judicial Council member Miriam Krinskey said.
"I leave it for the people to decide if that's a raise or not," he said.
Now that the proposal for the pay hikes has been formally submitted, the chief justice will decide whether or not to hand out the raises.