In July, an unreported surplus of $54 million was discovered in two special funds accounts in the parks department.
A later audit found accounting discrepancies in other state special funds.
The legislation is designed to prevent that from happening by requiring the state controller's office to use the same accounting methods as those used in preparing the Governor's budget.
The author of the legislation says the bill allows an "apples to apples" comparison.
But Republican Assembly member Diane Harkey thinks there is a better solution.
HARKEY: "This does not really go far enough, I think we need to remove the onus off of all the agencies and just get an outside audit like I know we can do."
The Assembly passed the bill on a party line vote, sending it to Governor Jerry Brown for his signature.