In the period between Christmas Eve and New Year’s Day, about 398,000 riders use the subway during the morning rush, compared with the roughly 713,800 riders on a typical weekday morning. During the evening rush, about 526,000 people ride the subway during the last week of the year, compared with about 644,300 riders the rest of the year.

The repairs will include laying 20,000 feet of cable to improve signals and replacing 2,000 feet of subway rails and 700 feet of track. It will also cost less to do the repairs all at once, said Phil Eng, the Transportation Authority’s chief operating officer, though he did not provide a precise amount. Weekend and night repairs, Mr. Eng said, increase the price of employing union laborers. Over 400 workers will be working in the tunnel.

“We have the opportunity to be more efficient and to make the best use of the taxpayer’s dollars,” Mr. Eng said. “These corrective repairs and maintenance will improve reliability.”

The tunnel shutdown is part of the $836 million Subway Action Plan, an ambitious overhaul being overseen by Joseph J. Lhota, the chairman of the Metropolitan Transportation Authority, since Mr. Cuomo declared the emergency in July.

“Riders understand that maintaining and upgrading the subway is going to require a certain amount of inconvenience,” said John Raskin, the executive director of the Riders Alliance, a transit advocacy group. “The trick is to minimize the disruption and to make sufficient progress in repairs.

He added, “Riders are willing to accommodate disruption in the short term if they are convinced they will have better service as a result.”

During the five days, the E train will not run on its usual track from the West Fourth Street station in Manhattan to the Roosevelt Avenue station in Queens, and instead it will run along the F line. There will be no M train service, except for shuttle trains between the Middle Village-Metropolitan Avenue station and the Myrtle-Wyckoff Avenues station in Brooklyn.