Brown said he wants more transparency and financial reporting from the school system. He also criticized administrators' salaries as being too high.
“I put the $50 million (the amount he is withholding) in there to hold their feet to the fire,” Brown said.
A state audit found that under university system President Janet Napolitano, former Department of Homeland Security chief, UC administrators hid $175 million from the public while increasing tuition and asking the state for more money.
The UC Board of Regents in January voted to increase in-state tuition and fees by $336 next academic year. Some lawmakers called for a reversal of the tuition hike in the wake of the audit.
When asked if he still has confidence in Napolitano as president, Brown defended her, saying the governing Board of Regents and others generally think she is doing a good job.
State Auditor Elaine Howle told lawmakers earlier this month that she faced an unprecedented lack of cooperation from Napolitano's office while it was under audit. She detailed efforts by the office to edit responses from individual UC campuses to survey questions from auditors.