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The MTA is working on a potentially historic reorganization plan that advocates fear could be rushed through without proper public review.

The reorganization has been billed as a means to bring significant restructuring to the MTA — which could include merging the authorities’ agencies — though there are still questions as to when it will be finished, how it will be shared publicly and how much time will be allowed for outside input.

“It’s difficult to determine exactly how the process will unfold, and that speaks to the need for more clarity about (the) plans (themselves),” said Rachael Fauss, of Reinvent Albany. “Overall, we’ve had concerns about the rushed timeline of the plan from the very beginning, and it’s incumbent upon the MTA and the governor to mitigate the fast timeline with a public process.”

On Tuesday, good government and transit nonprofits, including Reinvent Albany, penned a letter to Gov. Andrew Cuomo and the State Legislature calling for a more transparent look at the shaping of the reorganization — contracted out to the firm AlixPartners — and for ample time for its review.

The reorganization was mandated in the state budget, finalized at the end of March. Under law, the MTA is required to develop the plan in about three months, by June 30. But details on it and its scope have been scarce. The MTA’s board would be legally required to approve any major changes to the structure of the MTA outlined in the plan.

“We want to make sure we get this right. If [the restructuring] is rushed through behind closed doors — even if it’s a good plan that’s going to breed cynicism about it,” said Ben Fried, a spokesman for TransitCenter, another signee of the letter. “And that’s a recipe for a weaker plan — for it to not be fully vetted by transit experts. It would be a missed opportunity to bring any flaws to the plan and surface and good ideas to the public.”

While NYC Transit president Andy Byford is slowly but steadily stabilizing MTA subway service — at least during peak hours — Gov. Cuomo has repeatedly hammered the MTA over poor management and has talked up the restructuring.

“The MTA has to do a total reorganization plan by the end of this month, which is a fundamental reorganization of the institution,” Cuomo said at a news conference Monday. “Not a convenient one, not one that doesn’t rock any boats. They really need to reorganize that place, ground up, because it doesn’t work.”

The letter includes a recommendation to empower Byford to carry out his own modernization plan for transit service, known as Fast Forward. The restructuring comes at a critical time for the agency as it wades through a financial crisis, facing both operating and capital budget gaps. Even with congestion pricing and the new taxes secured in the state budget, the MTA is still struggling to get out of the red and fund big projects, which transit systems around the world manage to execute at much cheaper rates.

Andrew Albert, a nonvoting member of the MTA board, said it wasn’t yet clear to him when reorganization proposals will come to the board. But he felt confident, given MTA chairman Pat Foye’s commitment to improving transparency at the authority.

“Chairman Foye has sort of spoken to the issue of transparency,” Albert said. “So it would be ironic if this very important step in MTA history wasn’t transparent.”

The letter was also signed by StreetsPAC, Riders Alliance, Tri-State Transportation Campaign, New York League of Conservation Voters, Regional Plan Association and the Pratt Center for Community Development.

"As required by those reforms, we hired a world class firm, AlixPartners, to develop a reorganization and financial management plan which will be reviewed by the board and made public shortly after," said MTA Spokesman Max Young. "We appreciate the views and input of these groups, many of whom Alix met at the MTA’s request, and we are moving forward with developing this plan because it’s a new day at the MTA and New Yorkers shouldn’t have to wait any longer for these critical reforms."