The Federal Aviation Administration lifted its emergency order reducing the number of flights at many airports across the U.S., including Boston, allowing air traffic to return to normal on Monday after cuts during the government shutdown.

U.S. Transportation Secretary Sean P. Duffy and FAA Administrator Bryan Bedford made the announcement Sunday night. Normal operations at airports across the nation resumed at 6 a.m. Monday.

But Jennifer Mehigan, a spokesperson for the Massachusetts Port Authority, which operates Boston Logan International Airport, told The Boston Globe it would take “a few days for airlines to get their crews and aircraft back to a regular schedule.”

Mehigan did not immediately respond to a request for comment sent by MassLive Monday morning.

Bedford said the order reflected the “steady decline in staffing concerns across the [nation] and allows us to return to normal operations.”

The flight cuts started at 4% and later grew to 6% before the FAA on Friday rolled the restrictions back to 3%, citing continued improvements in air traffic controller staffing since the record 43-day shutdown ended on Nov. 12.

As of 7:30 a.m. Monday, 13 flights into and out of Logan airport were delayed and none were canceled, according to the flight tracking website FlightAware. On Sunday, 164 flights were delayed and nine were canceled.

Citing safety concerns as staffing shortages grew at air traffic control facilities during the shutdown, the FAA issued an unprecedented order to limit traffic in the skies. It had been in place since Nov. 7, affecting thousands of flights across the country.

Impacted airports included large hubs in New York, Chicago, Los Angeles and Atlanta.

The number of flights canceled this weekend was at its lowest point since the order took effect and was well below the 3% cuts FAA was requiring for Saturday and Sunday. Data from aviation analytics firm Cirium showed that less than 1% of all flights were canceled this weekend. The flight tracking website FlightAware said 149 flights were cut Sunday and 315 were canceled on Saturday.

The FAA statement said an agency safety team recommended the order be rescinded after “detailed reviews of safety trends and the steady decline of staffing-trigger events in air traffic control facilities.”

The statement said the FAA “is aware of reports of non-compliance by carriers over the course of the emergency order. The agency is reviewing and assessing enforcement options.” It did not elaborate.

Cancellations hit their highest point Nov. 9, when airlines cut more than 2,900 flights because of the FAA order, ongoing controller shortages and severe weather in parts of the country. Conditions began to improve throughout last week as more controllers returned to work amid news that Congress was close to a deal to end the shutdown. That progress also prompted the FAA to pause plans for further rate increases.

The agency had initially aimed for a 10% reduction in flights. Duffy had said worrisome safety data showed the move was necessary to ease pressure on the aviation system and help manage worsening staffing shortages at air traffic control facilities as the shutdown entered its second month and flight disruptions began to pile up.

Air traffic controllers were among the federal employees who had to continue working without pay throughout the shutdown. They missed two paychecks during the impasse.

Duffy hasn’t shared the specific safety data that prompted the cuts, but he cited reports during the shutdown of planes getting too close in the air, more runway incursions and pilot concerns about controllers’ responses.

Airline leaders have expressed optimism that operations would rebound in time for the Thanksgiving travel period after the FAA lifted its order.