If the city takes over the subways, it’ll have to run them without the $10 billion that the state provides the system, Gov. Andrew Cuomo said Wednesday.

His comments effectively torpedoed a plan proposed by City Council Speaker Corey Johnson 24 hours earlier for a new “Big Apple Transit” system run by the mayor, instead of the state-run MTA.

“Why hasn’t a mayor taken it over? There are about 10 billion reasons. That’s the $10 billion the state gives to the MTA, primarily New York City Transit Authority between operating and capital,” Cuomo said on WAMC radio.

“If New York City took it over, they take it over. They don’t get the $10 billion in state funding.”

Cuomo was then asked about why the mayor should have authority over the city’s public school system but not mass transit.

He said it comes down to the money: While Albany helps fund local schools, the city provides the lion’s share of the dollars, which isn’t the case with transit.

Cuomo also said that New York City actually owns and leases the subway system to the MTA and could give a year’s notice to cancel the deal.

“Just cancel the lease,” said Cuomo. “You don’t need to take it over.”

That wouldn’t make much sense because, without the state’s funding, the city couldn’t run the system.

Johnson, who is mulling a run for mayor, said Tuesday it’s better for bus and subway service to be overseen by a City Hall-run agency.

Johnson responded, “First off I’m glad to see the Governor is admitting he controls the MTA. As to those $10 billion reasons, New York City taxpayers and subway and bus riders are the ones who fund the lion’s share of the MTA already – the problem is we get no control in return.

“New York City is the economic engine of the state. We deserve control over how our money is spent and how our mass transit system is managed.”

Additional reporting by Danielle Furfaro