The Metropolitan Transportation Authority’s board on Wednesday approved a reorganization plan for the beleaguered agency — despite members’ concerns that the plan remains unfinished and could strip power from popular subways boss Andy Byford.

Boosters hope the controversial plan, which passed by a 10-1 vote with one abstention, will cut costs by $500 million a year by combining portions of the MTA’s famously unwieldy bureaucracy into centralized functions.

“What we’re going to take a vote on today is basically a road map,” said board member Larry Schwartz, a onetime aide to Gov. Andrew Cuomo. “You learn as you go.”

The pressure for the MTA to find new savings only grew Wednesday as the agency disclosed that its anticipated deficit through 2022 has grown by $447 million since its most recent budget update in February.

Without the consolidation, the agency anticipates deficits of $971 million by 2023 — however, even with the plan’s recommendations, it will still be $433 million in the red.

The plan recommends reducing the size of the massive 75,000-person agency by 3 to 4 percent — around 1,900 to 2,700 staffers — and relocating many operations from agencies to MTA headquarters.

But straphanger advocates and good government groups assailed the proposal as half-baked, saying it could wrestle important construction and engineering powers away from the MTA’s division chiefs, including Byford.

“We consistently hear that separating functions like capital construction and engineering from the operating divisions will create disorganized chains of command, causing higher costs, more project delays and worse service disruptions,” said Ben Fried, a top advocate for mass transit advocacy group TransitCenter.

“Yet, that is what this report recommends.”

Advocates fear the plan will strip Byford of control of his $40 billion “Fast Forward” plan to overhaul and computerize the decrepit, decades-old subway signal system that regularly cripples service.

Representatives from the consulting firm that assembled the plan, AlixPartners, suggested the signal revamp would likely continue when quizzed by city-appointed board member Veronica Vanterpool — who cast the lone no vote — but declined to provide a definitive answer.

“Anything that is already underway or anything that is very specific to an agency will probably stay there,” said the firm’s Foster Finley.

However, he added, the final call would rest with MTA’s new “Transformation Director,” a position created by state lawmakers at Cuomo’s behest that answers to the board.

Cuomo reportedly has an icy relationship with Byford, who has garnered headlines and praise for the signal fix-up as well as dramatic improvements in on-time performance in recent months.

But MTA chairman Pat Foye dismissed concerns that the signaling effort will be hindered by the reorganization.

“The Fast Forward program is already working towards planning and designing for resignaling,” Foye said at a press conference after the board meeting.