SACRAMENTO — Details of a tentative state budget agreement between California lawmakers and Gov. Jerry Brown remained in flux late Monday afternoon, as negotiators scrambled to meet a new voter-mandated deadline.

The Legislature has until Thursday to pass the state’s 2017 budget, but they are laboring under a new wrinkle: Monday is the last day they can make changes to the main budget bill if they want to meet the June 15 constitutional deadline — and get paid. That’s because California bills now must be in print for a full 72 hours before they can be put to a floor vote, thanks to a constitutional amendment voters approved in November, Proposition 54.

“I think it’s fair to say it has made the process more compressed,” said H.D. Palmer, a spokesman for the Department of Finance, about the new rules.

As of 4 p.m. Monday, the bill still included an expansion of a state tax credit program for low-wage workers and the self-employed as well as the Middle Class Scholarship — a tuition discount for middle-income college students that Brown has proposed eliminating.

Last month, Brown unveiled a $124 billion state budget proposal with a slightly rosier budget outlook than his original blueprint a few months earlier. He proposed giving more money to schools and restored a previously promised $500 million increase in funding for subsidized child care. But the governor in May held the line on putting more general fund dollars to the construction of affordable housing, as lawmakers had wanted.

“I don’t think we should throw money at the housing problem if we don’t adopt real changes that make housing production more efficient and less costly,” Brown said at the time.

Brown also proposed withholding $50 million from the University of California — pending fiscal reforms agreed upon after a highly critical state audit — to “hold their feet to the fire.”

The Legislature wanted to go further, directly funding the university system’s central administration — taking that authority away from the UC Board of Regents — as a way of keeping stricter oversight. As of late afternoon Monday, the main budget bill included that provision, over the university’s objections.

“We continue to believe that the UC Board of Regents is best placed to provide fiduciary oversight to the Office of the President,” said UC spokesman Ricardo Vazquez.

Another point of contention in budget negotiations is how the state will spend money from its new tobacco tax. The matter is being hashed out in a separate bill, Senate Bill 105. Brown has proposed using the tobacco tax revenues to cover general fund expenses in the Medi-Cal program.

But doctors say the money should go to raising California’s reimbursement rates for doctors who accept Medi-Cal. California Medical Association President Ruth E. Haskins has said Brown’s proposal ignores “the clear language of the tobacco tax initiative (Proposition 56) and the will of California voters.’’

Under the current rates, Haskins and other physicians say, many California doctors say they can’t afford to see Medi-Cal patients. In a state where more than a third of Californians, including 50 percent of children in the state, rely on Medi-Cal for health care, Haskins has said offering increased coverage doesn’t do much if patients are forced to wait months to get an appointment with a physician or dentist, can’t access a specialist, or have to travel greater distances to their medical appointments.

In a statement Monday afternoon, CMA spokeswoman Joanne Adams said: “On first glance this legislation raises more questions than it answers. We will provide more comment once we have thoroughly reviewed.”\xe2\x80\x8b

Lawmakers also want to expand Medi-Cal to include undocumented young adults.

Under another budget-related bill, the state’s troubled tax board, the Board of Equalization, would lose almost all of its power, and the state would instead create a new revenue department, California Department of Tax and Fee Administration. Its director would be appointed by the governor.

An audit released this spring by the Department of Finance found that board members interfered with daily operations and redirected staffers to work on their outreach projects, among other problems. Brown sanctioned the board after the audit and asked state lawmakers to respond to the audit findings. The governor also asked Attorney General Xavier Becerra to conduct another investigation.

Board member and former state Assemblywoman Fiona Ma, who has publicly criticized the agency, said in a news release Monday that she supported the reform proposal outlined in Senate Bill 86.

“I commend the Governor and the Legislature,” she wrote, “for providing the necessary corrective action to steer the BOE in the right direction to restore the public’s trust in the hard work being done by this agency.”