The loss of fare revenue due to lower ridership “will destroy the MTA” if the state doesn’t step in to provide funding for the cash-strapped transit system, a government watchdog said Wednesday.

The warning, included in a new report from good government group Reinvent Albany, came after transit leaders also sounded the alarm about the authority’s $18 billion-per-year budget.

“We believe the decline in fare revenue, combined with an end to federal COVID operating aid and historically high debt levels, will destroy the MTA and transit service unless the state delivers the MTA billions in new dedicated operating funds,” the report read.

Ridership levels dropped over 90% in the initial weeks of the pandemic and are expected to remain as low as just 73% of pre-pandemic levels come the middle of 202 — costing the MTA $200 million each month, the report said.

A $15 billion cumulative infusion of federal cash over 2020 and 2021 temporarily secured the MTA’s budget — but only until 2024. The MTA’s budget is further hamstrung by over $40 billion in debt, which is pays off in part with money from rider fares, the report said.

“It’s no secret the MTA’s debt loads are unsustainable,” Reinvent Albany analyst Rachael Fauss told The Post. “The federal funding has, in some ways, masked how bad it is.”

Transit leaders have been warning about the MTA’s finances since the start of COVID, saying that they will have to make devastating service and jobs cuts without additional funding.

MTA CEO Lieber met with lawmakers about the looming “fiscal cliff” during the Somos conference in Puerto Rico last week, non-profit news outlet The City reported on Friday. He has also spoken with City Council members, the report said.

“We agree the MTA needs new dedicated funding and the fiscal cliff is real and appreciate Reinvent Albany’s passionate advocacy for investment in mass transit,” MTA spokesman Aaron Donovan said in a statement.

Albany and City Hall may be Lieber’s only option to save the MTA with Republicans taking control of the House of Representatives, according to one insider.

“The next two years in Washington are going to be deadlocked,” the source said. “There aren’t going to be operating subsidies with the new Republican House.”