The union says so far it can't verify the MTA's figures, but according to the MTA, 25 percent of its workers called in sick 15 or more days last year.
All employees are entitled to 12 sick days.
That's on top of an average 37 days of vacation time and holidays each year.
But now the cash-strapped agency says it simply can't afford all this.
More than 400 station agents have been laid off, and more layoffs are coming.
There is a court fight to try scale back a recent raise, and now the vow to cut back on overtime.
"Overtime is a critical part of our business it always will be, but when we looked at the overtime we found a lot of it was unnecessary," said Jeremy Soffin, an spokesperson for the MTA.
The MTA says it simply can't afford $560 million a year on overtime, so the agency's now hoping to slash $22 million out of this year's labor budget and another $60 million next year.
"The reality is when you're down to your last dollar you have to make sure that every dollar is really accounted and things that may have been okay in different economic times aren't now," adds Soffin.
But by trying to slash overtime, MTA leaders have waded into a hornet's nest of anger.
"These are pampered bureaucrats and they never did a full days work in their lives they'd faint, if they had to come into the subway and do what do every night they would faint," said John Samuelson, TWU local 100 President.
Samuelson is livid at MTA leadership, claiming the agency went to reporters before them on a plan to cut overtime.
Local 100 says so many workers call in sick because they work in horrible conditions.
"We work around homeless people and we work around fecal matter. We breathe in toxic chemicals, steel dust, creosote, manganese, and transit workers get sick. And when we get sick we take sick time and we're not going to apologize for that," adds Samuelson.
The MTA's overtime report also found that 16 percent of its bus and subway workers didn't call in sick for even one day last year.
Still the agency's trying to crack down on other workers who might be calling in sick when they really aren't.
The MTA also wants to change some rules like a commuter train operator getting an extra day's pay when going from a diesel to an electric train.