Maybe the MTA isn’t so broke after all.

A new audit found over $90 million in unaccounted funds that could have been used for the MTA’s operating budget.

New York state comptroller Thomas DiNapoli also found that the MTA wasn’t documenting whether it was getting the maximum returns on its investments.

“The MTA is leaving money on the table and in these tough times, every dollar counts,” DiNapoli said.

“Our auditors identified several ways in which the MTA could vastly improve how it manages its cash and investments. The MTA must do better.”

The MTA has $1.8 billion in 126 different bank funds, all of which are used to hold money for different agency expenditures.

The comptroller’s office looked at ten of those funds totalling $881.2 million.

Auditors found that in some cases, there was more money than necessary in the accounts.

In one instance, an account dedicated to fund capital expenditures for bridges and tunnels was required to have a total of $160 million.

The auditors found that the fund actually held $216.3 million, an excess of $56.3 million.

That extra money should have been included in the agency’s budget, DiNapoli said.

An MTA spokesman said the extra money was needed to keep the agency’s credit rating up.

“Monies in this account are essential to maintaining our credit rating, and are available in the event of emergencies such as Superstorm Sandy,” said MTA spokesman Kevin Ortiz.

He said the agency is making changes to how it manages its funds and expects to achieve greater efficiencies, a process that was underway before the comptroller prepared its findings.

“We expect numerous accounts will be closed or consolidated,” he said.

The MTA plans to raise fares next month. The fare hikes will bring in an extra $382 million in extra revenue this year.

jennifer.fermino@nypost.com