Published reports suggest that special funds in other departments could be off as much as $2.3 billion.
H.D. Palmer with the state's finance department says those reports are inaccurate and incomplete.
He says almost $500 million of that is the result of differences in accounting methods used by the controller's office and the finance department. He believes their audit will prove that.
PALMER:"Can we say with certainty today that we are not going to find an anomaly like we found last week with the two parks funds? Absolutely not, but that's exactly why Governor Brown directed us to look at each and every one of these funds."
But Republican Jim Nielsen, Vice Chair of the Assembly Budget Committee, says whatever the problem, it needs to be fixed.
Nielsen: "Something is very very wrong period, and it's been wrong for a long time and it cannot be tolerated anymore."
Nielsen and other lawmakers have called for hearings into the financial problems beginning in August.
Democrat Mark Leno, Chair of the Senate Budget Committee says its too early to know the exact discrepancies in the state's special funds.
LENO: "But the fact remains that under state law these dollars cannot be used to address the ongoing structural imbalance in our General Fund, which the Legislature has taken significant steps to reduce in recent years."
Leno says he's encouraged that the Brown Administration and the Finance Department have immediately taken steps to correct the situation, which he says "they inherited from previous administrations."