The MTA is ramming through Gov. Andrew Cuomo’s controversial plan to avert the L train shutdown, the authority announced Thursday — just two days after the agency’s board bashed the plan during a heated “emergency” meeting Tuesday.

“[T]he total shutdown of both tunnels and all service scheduled for April 27 will not be necessary,” reads a statement issued by the MTA Thursday evening.

An MTA insider said the announcement had Cuomo’s fingerprints all over it.

“Cuomo is saying he knows more about the technology stuff than the technology experts on the MTA board,” the official said. “It’s just a demonstration of who runs the show. This is Cuomo being completely dominant over the MTA.”

The MTA will attempt the legal maneuver by arguing that no board approval is needed because it claims Cuomo’s new plan won’t cost more than the original shut down, even as the embattled authority continues to refuse to provide a price tag.

Good government groups assailed the move.

“The Governor is a wrecking ball, destroying public confidence in both the MTA professional staff and himself,” raged John Kaehny, the executive director of Reinvent Albany. “If the board has a shred of authority, it should be voting on this very major decision.”

The Canarsie tunnel carrying the L train from Brooklyn to Manhattan was scheduled to be closed for 15 months of post-Hurricane Sandy repairs, but Cuomo swooped in on Jan. 3 and announced the authority would instead shutter one tunnel at a time for piecemeal repair.

Then he pumped the brakes the next day and said the MTA board needed to approve the proposal. But the board picked apart the plan Tuesday over concerns the fix wouldn’t last as long as the initial plan — and would expose riders to carcinogenic silica dust.

“We’re starting out marginally less safe,” the MTA source said. “And that’s not a good place to start.”

The news came just hours after Cuomo once again argued on WNYC radio that he should be in charge of the struggling authority — which he already controls.

“Many people are wrong,” he told host Brian Lehrer, when asked about the claims. “We live in a world of tweets, where facts don’t matter.”

Hours later, Cuomo’s MTA announced the end-run around its own board.

The governor’s office did not respond to a request for comment.