The MTA will lay off more than 600 employees represented by nine different unions in the next two months, the agency said yesterday.

Those cuts are part of the agency’s plan to save $62.2 million of a $750 million budget shortfall.

Also facing the ax are about 527 other administrative employees who are not unionized.

“I feel badly about that but I truly don’t see any choice — it’s going to be a very difficult year for all of us,” MTA chief Jay Walder said yesterday.

“I sometimes feel like we’re running up the down escalator” in terms of cutting costs, he added.