The MTA needs to improve service through system maintenance and modernization for long-term revenue — rather than quick-fix fare hikes and job cuts, a new budget analysis from State Comptroller Tom DiNapoli found.

But the agency’s “budget reduction plan” currently takes the opposite approach in the form fare increases, maintenance worker job cuts and possibly service reductions — all of which may have the “unintended consequence” of scaring off even more riders, according to the report released Friday.

The MTA has lost $250 million annually since 2016 due to declining bus and subway ridership, and faces looming deficits approaching $1 billion in the coming years.

At the same time, the outcome of the “transformation plan” approved by the MTA board in July, which also relies on job cuts to yield hundreds of millions of dollars in savings, remains uncertain. And while MTA officials have said their $62 million fare enforcement effort will re-coup funds, the agency’s July financial plan made no mention of any additional revenue from reduced fare-beating.

“The transformation plan and the budget reduction program both require close monitoring to ensure that planned savings materialize and that unintended consequences, such as reductions in service reliability, are avoided,” DiNapoli’s report said.

However, the report argued, “If the MTA continues to improve service and limits future fare increases, it may encourage riders to return, increasing revenue beyond the current forecast.”

The MTA has already cut service on a handful of under-performing, infrequent bus routes. More cuts could be coming down the pike.

The cuts reflect what MTA buses and subways chief Andy Byford has called a potential “death spiral” — where declining ridership begets service cuts, which in turn exacerbates declining ridership.

“Service cuts hurt riders and are not in the long term financial interests of the MTA,” Riders Alliance Political Director Rebecca Bailin told The Post. “As the comptroller implies in his report, cutting service could lead to less revenue, the last thing the MTA needs right now.”

On Thursday, Byford told reporters at an unrelated press conference that service cuts are an “anathema” to him.

“We came here to improve service, not to cut service,” Byford said. “Having said that, I’m not going to sugarcoat this. We do face a real financial challenge in the short and medium terms.”