The MTA is desperately fighting the Trump administration to keep collecting its congestion-pricing tax — but a hefty chunk of the nearly $40 million a month in new tolls isn’t going to shore up the city’s dilapidated transit system: Instead, $1 million is siphoned off by private payment companies — like Visa, MasterCard and banks — that make big bucks off small transactions.

A little-noticed February oral report to the MTA board revealed, for the first time, just how big that previously secret number must be.

What’s more, it’s not just congestion pricing: The finance companies are taking a substantial cut of every single subway swipe, bus ride, Metro-North ticket or LIRR pass charged to a debit or credit card — potentially hundreds of millions of dollars a year. 

The issue involves “interchange fees,” a charge levied on every debit- or credit-card transaction.

Federal rules limit those debit-card fees to between 22 and 50 cents. But the fee is the same for both big-ticket items and small “micropayments” — like a subway swipe. (Merchant fee pricing on credit cards, which isn’t federally regulated, varies widely.)

In its official budget, the MTA doesn’t list such costs as a separate line. Citing non-disclosure agreements, it won’t........

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