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The fight between Gov. Sam Brownback of Kansas and the state’s judicial branch has escalated, with the governor last week signing into law a bill that could strip state courts of their funding.

The measure, at the end of a lengthy bill that allocated money for the judiciary this year, stipulates that if a state court strikes down a 2014 law that removed some powers from the State Supreme Court, the judiciary will lose its funding.

The 2014 law took the authority to appoint chief judges for the district courts away from the Supreme Court and gave it to the district courts themselves. It also deprived the state’s highest court of the right to set district court budgets. Critics said the law was an attempt by Mr. Brownback, a Republican, to stack the district courts with judges who may be more favorable to his policies.

The budget bill that Mr. Brownback signed on Thursday was related only to the judiciary. He said he wanted to ensure that the courts would remain open while lawmakers sparred over the larger budget issues. Lawmakers have been debating how to fill a $400 million shortfall, which will most likely require tax increases that Mr. Brownback and many in the conservative-dominated Legislature oppose. If a budget is not passed by Sunday, state workers may be furloughed.

But in passing a separate budget bill to keep the third branch of government from shutting down, Republican lawmakers took the opportunity to insert language that would shield the 2014 law.

“I’ve never seen anything like this,” said Matthew Menendez, counsel at the Brennan Center for Justice in New York, which is helping to represent a Kansas judge who is challenging the constitutionality of the 2014 law. “It seems pretty clear that these mechanisms have been an effort by the governor and the Legislature to try and get a court system that is more in line with their philosophy.”

Richard E. Levy, a constitutional law professor at the University of Kansas, likened the measure in the judiciary budget bill to Congress’s passing a law outlawing abortion and then telling the judicial branch that it will lose its funding if it finds the law unconstitutional.

“That kind of threat to the independence of the judiciary strikes me as invalid under the separation of powers principle,” Mr. Levy said in an interview on Friday.

The 2014 law was promoted by the Legislature’s conservative bloc, whose members argued that the local district courts would better know the needs of their communities and should, therefore, have control over their own purses and leaders. Jeff King, the vice president of the Senate, told The Wichita Eagle at the time the law passed that it was not an attack on the courts because the measure did not give the Legislature any authority over the courts.

The very same state court system that will be affected by the 2014 law will decide whether the law is constitutional. The Brennan Center, which is representing Judge Larry T. Solomon, the chief judge of Kingman County in south-central Kansas, has argued that the law violates a provision of the State Constitution that says the Supreme Court “shall have general administrative authority over all courts in this state.”

“If the people of Kansas were to adopt a constitutional amendment that changed the way that the courts were administered, I think that would be a very different situation,” Mr. Menendez said Friday.

But the office of Attorney General Derek Schmidt has argued in court filings that Judge Solomon does not have standing to bring a claim and that the Legislature has the constitutional authority to determine how chief judges are selected.

“Chief Judge Solomon has not been injured in any personal and individual way,” the attorney general’s office wrote in a motion to dismiss the lawsuit. Later, citing the fact that the Legislature had been allowed to create a statute governing jury selection, the motion argued, “It is clear that the authority to regulate court administration and procedure is not vested exclusively in the Kansas Supreme Court.”

The Kansas courts and Legislature have been at odds in recent years. Lawmakers have challenged judicial rulings that the state’s school system was constitutionally underfunded, arguing that the courts were impeding on the legislative authority to appropriate money. Some lawmakers have said they would openly defy any court ruling that says they must provide additional school funding.

Mr. Brownback and his Republican allies who control the Legislature have sought to change the way that State Supreme Court justices are selected, proposing a system in which the governor would nominate a candidate and the Senate would confirm the person, similar to the federal model. The governor has also suggested the possibility of going to direct elections for Supreme Court seats.

Under the current system, the governor chooses from three nominees picked by a nine-member committee that includes lawyers and appointees of the governor.