People arrived at the Registry of Motor Vehicles office on Blackstone Street in Boston were informed that their estimated wait time would be four hours. Jim Davis/Globe Staff)

Motorists faced crushing waits as long as five hours at Registry of Motor Vehicles branches on Monday, the first day of a new driver’s licensing system in Massachusetts.

RMV employees at the downtown Boston branch were warning customers of lengthy delays and suggesting they come back the following day.

“It’s as long as we’ve ever seen it,” a registry employee told customers as they tried to enter.

Transportation Secretary Stephanie Pollack acknowledged that many motorists statewide faced long waits, and few were waiting less than 30 minutes, the RMV’s target for processing most applications.

“Lines are longer than we’d like them to be. We’d expect that to continue for a while and then to calm down as folks get more experienced with the system,” Pollack said.

The trigger for the big backup was a different system and protocol for issuing a new type of driver’s license, Real ID, that requires motorists to apply in person and provide more extensive proof of identity. The RMV closed its doors and online systems for three days starting Thursday night to prepare for the new process.

But on Monday, the first day back in service, the delays affected everyone with business before the registry — those who needed new licenses, as well as those who came to renew permits or registrations.

“I thought it would be 40 minutes, the usual wait,” said Abdull Abdullah, a 21-year-old Jamaica Plain resident who waited 2½ hours to test for his learner’s permit before calling it quits Monday. “I had plans. I had stuff to do. And I was pretty sure I was going to pass.”

When the RMV reopened Monday morning, Pollack said, the new software worked fine. But it is taking longer for employees to process Real ID license applications, which require motorists to produce a combination of Social Security card or work documents, passport, certified copy of a birth certificate or immigration papers, and proof of Massachusetts residency.

“It’s just new for both employees and customers,” Pollack said. “The actual process when you have a person and a pile of documents is taking longer than it used to take when you renew a license. . . . Our transaction times are definitely longer than they have been on average.”

Customers waited in line Monday at the downtown Boston RMV office. Jim Davis/Globe Staff

Meanwhile, more people came to registry branches Monday for business that they couldn’t conduct during the closure Friday. For example, the registry had a higher number of people in Monday for registration renewals, Pollack said.

AAA members also faced longer waits at its locations that offer RMV services because of the “learning curve” of the new system and additional document requirements, spokeswoman Mary Maguire said.

The huge backups are a reminder of the old days of the registry, which has aggressively tried to overcome a reputation as the quintessential plodding government agency. Its goal is to serve 80 percent of customers in 30 minutes or less, and in the first two months of 2018 the RMV reported that more than 90 percent of waits were under a half hour.

Downtown Boston was the extreme example Monday, with an average wait time of 2 hours and 23 minutes, according to state figures released Monday night. The average statewide was 1 hour and 20 minutes, with the Roslindale and Watertown branches also approaching two hours. Meanwhile, down in Nantucket, drivers were served in under 10 minutes.

In Boston, Quincy resident Eveline Lopes promptly turned around and left after hearing how long the wait would last and plans to return Tuesday. Employees told her she might have better luck trying to renew her license in the morning, but because of her work hours, she cannot return until the afternoon. She’s not optimistic Tuesday afternoon will be much better.

“Instead of five hours, hopefully it will just be two to three hours,” Lopes said.

Some drivers stuck out the waits and successfully applied for the Real ID. Kenny Jervis said he only waited 1½ hours Thursday downtown and had little trouble getting a Real ID license. There was a small glitch as the system didn’t recognize his middle name, he said, but registry staff was able to work around it.

Drivers must go to RMV branches or AAA locations to obtain a Real ID, but they can kickstart the process by filling out a pre-application on the RMV website, which — in theory — should shorten the time spent at the registry.

Under federal rules, Real ID will be the only type of driver’s licenses accepted for identification to board a flight or enter a federal facility after October 2020. Those without a Real ID will need to use passports or other federal identifications to board flights after 2020. Officials say residents should visit mass.gov/id to learn about the license requirements.

Drivers can renew a standard, non-Real ID Massachusetts license online, but those also require additional proof of residency and citizenship; both types of licenses cost $50.

The RMV has stressed that drivers don’t need to rush in for a Real ID, because they are not required for federal purposes for more than two years. Instead, they can come in as their license expires. Still, the registry is anticipating longer wait times as people come in for Real IDs, even if the system worked perfectly.

Some drivers on Monday were aware of the changes to license requirements, while others were not. Sasa Epiphany of Boston came to renew a permit but did not know she needed her passport and will have to return on another day.

Others, such as Tim Rice of Boston, were overly prepared. Rice stood in the lobby of the Boston RMV clutching his passport, utility bill, bank statement, and other documents with his address, just in case. “I’ve been trying to understand it,” he said of Real ID.

The transition has faced several problems. Some drivers whose licenses expire this spring and summer are complaining about a recent letter from the RMV encouraging them to renew their standard Massachusetts license online early without alerting them to the Real ID option.

The transition to Real ID also drew a small protest outside the Boston RMV branch Monday from activists with the Boston May Day Coalition, who said motorists should not be required to show proof of citizenship or immigration papers to obtain a license. While the RMV has always required these documents for a license, in Massachusetts, a 2016 law more clearly defined the requirement.