The MTA is making a “giant mistake” in going over its board members’ heads to implement Gov. Cuomo’s controversial ­L-train repair plan in the face of intense pushback, one of those board members raged Thursday.

“Board approval is the proper way to proceed,” Andrew Saul said during a heated meeting.

“I don’t see how we can make a change without the board … to approve this action.”

Cuomo-appointed acting board Chairman Fernando Ferrer didn’t directly address Saul’s demand, but insisted “nothing will be done in the dark of night.”

Never mind the fact that the MTA first announced the plan was going full steam ahead with a press release at 5:55 p.m. last week.

“As acting CEO, I’m not going to delay this project one day if I don’t have to,” Ferrer said.

Repairs were slated to begin April 27 under the old plan, but some board members are skeptical the new course of action can be vetted and implemented by then, signaling that delays may be in store for the plan anyhow.

The MTA initially intended to close the L-train tunnel that links Brooklyn and Manhattan for 15 months of Hurricane Sandy repairs starting in April, but Cuomo announced an alternative plan on Jan. 3 that retains 24/7 service but cuts corners on repairs and relies on reduced night and weekend service.

The MTA promptly changed course in favor of the governor’s plan — first indicating it was subject to a board vote before ultimately announcing the plan would move forward without a ballot.

A draft memo leaked Wednesday shows that the authority is considering yanking extra buses and subway service it had planned to mitigate the pain of a full L shutdown.

Cuomo claimed he never saw the memo, but nonetheless defended its conclusions.

“So, all the alternatives are not now necessary because you’re not stopping the L train,” he said Thursday.

An MTA rep said “far less alternate service will be needed” now that the shutdown will be averted.

Asked why the governor — who swears up and down that he doesn’t control the MTA — always “wins” when it comes to the transit agency, Ferrer replied, “Maybe because he’s the governor?”