The MTA chief shot down raises for the labor unions without concessions at a state hearing on Thursday — saying such a wage boost would sock riders with a large fare hike.

Chairman Thomas Prendergast said the financial hit to the MTA would be equivalent to a 12 percent fare hike if all unions got an almost 3 percent raise without changes to archaic work rules.

This was the amount recommended for the LIRR by a President Obama-appointed emergency board to solve an impasse between the LIRR and MTA.

“That would be a terrible choice,”  Prendergast said, and added that all new labor contracts would have net zero wage increases.

“Employees deserve raises, but we need to do that in a way that balances our budget and doesn’t put our financial plan in risk.”

Fares are scheduled to go up to 4 percent in 2015 and 2017, he also said in the hearing. They were slashed from 7.5 percent in December after the MTA’s finances have improved due to cost-cutting, as well as higher ridership and lower-than-expected healthcare and pension costs.