Gov. Andrew M. Cuomo, who in the past has touted his control over New York City’s subway system, doubled down Thursday on his argument that New York City, not the state, is responsible for funding upgrades to its beleaguered subway system.

Cuomo had previously ordered the city’s subway system to be shut down in advance of superstorm Sandy, citing his authority over the system, and led the inaugural ride of the Second Avenue subway line by lauding the state’s work on the effort.

Cuomo, and newly appointed MTA Chairman Joe Lhota, in separate events Thursday said the city is in charge of financing the subway system’s capital improvement plan, despite the state Metropolitan Transportation Authority controlling the day-to-day operations of the aging subway system.

Speaking to reporters after an unrelated bill-signing ceremony in lower Manhattan, Cuomo said, “it’s the city’s legal obligation to be funding” subway upgrades and improvements, “even though we stepped in on a moral level” to provide state funding.

Meanwhile, a spokesman for New York City Mayor Bill de Blasio, accused the governor of peddling “diversions,” and said the city has invested $2.5 billion toward the subway’s five-year capital improvement plan.

The back-and-forth over spending comes amid growing frustration from commuters dealing with widespread delays and system malfunctions.

Cuomo’s comments came a day after de Blasio criticized the governor’s estimated $215 million plan to deck out local bridges with multicolored LED lights that could display animated light shows. Transit groups have said funds would be best spent on fixing the aging subways.

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Cuomo has said the light displays would serve as tourist attractions, but de Blasio Wednesday told reporters Wednesday subway riders are more “interested in getting the trains to run on time . . . and that’s what we should focus the resources on going forward.”

Lhota, in a hastily called afternoon news conference, said the city’s subways were “an affiliate” of the MTA, citing state laws from 1953 and 1981 to note the city owns the subway tracks and leases them to the MTA.

“I don’t want to get into politics. It’s not about personalities,” Lhota said. “It’s about who owns and who needs to provide the funding.”

De Blasio Spokesman Austin Finan, in a statement, said: “Let’s stop the diversions and obfuscation and start spending the resources the MTA has on the repairs and maintenance that will keep New Yorkers moving.”

On Thursday, Cuomo and de Blasio both spoke at the opening of a health care center in Brooklyn, but narrowly avoided each other. As Cuomo finished his remarks and walked out one door, de Blasio entered seconds later through another door to start his speech.