The upgrades are meant to enhance the reliability and security of processing debit and credit card transactions, according to the M.T.A. The city’s more than 2,700 MetroCard machines process about 800,000 transactions each day. A spokesman for the M.T.A., Shams Tarek, said the disruption was necessary to make the improvements. “It is like any computer, right?” he said. “You can’t operate a computer while you’re replacing the software.”

MetroCard machines were introduced at the turn of the century. In the last 14 years, there have been three major system upgrades, according to information provided by the agency. There are also periodic outages on Saturdays between 2 a.m. and 3 a.m. while the system is backed up.

“They are trying to extend the life of this equipment that truly should have been replaced by now,” said Richard Barone, the vice president for transportation for the Regional Plan Association, an urban research and policy organization. “We are working with equipment that is going to need continuing investment to continue to work.”

Corey Johnson, the City Council speaker, said the new schedule was an improvement. But the enraged reaction from riders pointed to the subway’s bigger problems, he said, of endemic delays, crumbling infrastructure and deep unreliability that led Gov. Andrew M. Cuomo, who controls the M.T.A., to declare a state of emergency and unfurl a $836 million plan last summer to turn around the troubled system.

“It is emblematic of just complete and total mutiny and unabated anger at the M.T.A. for the daily abuses that riders have to endure,” he said. “If this was an isolated incident on its own, people may have shrugged and dealt with it, but given everything else, this became a rallying cry.”

By 2023, MetroCards will be phased out entirely; fares will be paid with contactless readers that can deduct from credit and debit cards, similar to transit payment systems in London and other cities. Mr. Barone said that the new system would not likely need to be taken offline for updates. Unlike the MetroCard machines, which do much of the processing of transactions themselves, the new system will process payments in a back-end computer system.

The debacle over the upgrade, Mr. Johnson said, underscores the need for that more modern fare collection technology.

“In the meantime, things might be clunky and unacceptable,” he said. “But this is an improvement until we get a state-of-the-art technology system.”