Council Speaker Melissa Mark-Viverito admonished MTA Chairman Joe Lhota for not attending the hearing even though he had been asked several times to do so.
Once an MTA representative laid out the agency's plans to fix the troubled system, the focus turned to the problem of who will pay for the repairs and how much.
That issue triggered a testy exchange.
"This reality-based recovery program of essential repair work is truly an investment in the city's future, "said MTA Managing Director Veronique Hakim. "And we're asking for your help to insure that is jointly funded between the city and the state as chairman Lhota has proposed."
"I understand the MTA is a creature of the state and therefore you respond to the governor," said Mark-Viverito. "But to make it seem that the governor's being so magnanimous and that this city is rejecting its responsibility, I''m not going to sit here and accept that."
They continued to argue over how much money comes from the state versus how much comes from the city
Last week, Councilman Ydanis Rodriguez and State Assemblyman Jeffrey Dinowitz spent 24 hours on the subway between Thursday and Friday.
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Rodriguez will present the findings of his tour in which he listened to riders.
The Council will also discuss funding issues, including Mayor de Blasio's plan to tax the wealthiest residents to pay for subway repairs as well as other proposals, such as earmarking 2 percent of income tax revenues for mass transit and restoring the commuter tax.
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Rodriguez said the current funding proposal from the MTA is just a band-aid for right now and he is looking for more long-term solutions.
Lhota recently unveiled an emergency plan to stabilize the system at a cost of about $836 million.
Gov. Andrew Cuomo offered to split the cost of the plan with the city, but the mayor refused to commit money to support it.
The tax plan proposed by de Blasio, which would generate about $800 million annually, would increase the top income tax rate from about 3.9 percent to 4.4 percent for married couples who make more than $1 million and individuals making more than $500,000.
(The Associated Press contributed to this report.)