The average New York City Transit employee missed 54 days of work last year, according to data obtained by The Post — and experts say the high number is driving the agency’s skyrocketing overtime costs.

The internal data shows that among those days, workers for the MTA’s city subway and bus arm take an average of 18 vacation days, eight holidays, nine sick days and four training days — all paid.

Employees also took an average of six workers’ comp days and another five unpaid sick days, the data shows.

At the same time, the MTA’s overtime bill has jumped 36% since 2016 — up to $1 billion last year — and officials say the large amount of time workers are away is one of the reasons so much OT is needed.

The MTA faces deficits approaching $1 billion in the coming years, and as the agency enters into negotiations with its unions, experts says the provisions that allow for so much time away from work must change in order to rein in costs.

“The low average work year helps explain the overtime surge,” said E.J. McMahon of the Empire Center for Public Policy.

“Both of these problems underscore the need for MTA management to demand significant work rule changes in the coming round of contract talks with MTA unions.”

Much of the NYCT workers’ time off is guaranteed in the Transport Workers Union Local 100’s contract, which expired in May.

The contract gives every bus and subway worker a minimum of 10 vacation days per year — plus 10 more after three years of service and another five after 15 — as well as 12 paid sick days.

Workers are also entitled to nine public holidays — and, after one year of service, their birthdays.

MTA Chairman Pat Foye has also previously pinned high overtime costs on employee availability, and pointed to the negotiating table as one the place to address them.

“Availability impacts overtime because employees who are out must be back-filled, usually on overtime,” Foye said at the July MTA board meeting.

“Low levels of availability [are] largely the result of contractual math creating lower levels of availability and correspondingly high and growing levels of overtime,” he added.

TWU officials called Foye’s comments “callous, careless, or both.”

Labor leaders threw blame back at the agency for failing to protect workers from assaults and other injury-related incidents — the reason for about 11 percent of the work days missed.

“All workers, regardless of occupation, deserve a healthy work-life balance,” TWU Local 100 Vice President Eric Loegel said at the time. “We do dirty, dangerous, safety-sensitive jobs and need sufficient time to recover.”

The MTA’s overtime costs have been in the spotlight for months since the Empire Center revealed that some Long Island Rail Road workers last year received staggering sums of money while logging seemingly impossible overtime hours.

The MTA and TWU both declined to provide additional comment on the new data.