The US transportation department has lifted its emergency order to cut flights across the country, saying enough air traffic controllers are now coming to work to alleviate safety concerns.

During the government shutdown that started in October, there was a rise in absences of air traffic controllers, who – as essential employees – were required to work without pay, which led airports to delay or ground flights.

The Federal Aviation Administration (FAA) then ordered airlines from 7 November to cut scheduled takeoffs in order to prevent safety issues.

Since the shutdown ended last week, staffing levels “have continued to snap back”, the department said, just in time for busy Thanksgiving travel.

More than 6 million people in the US are expected to fly during the Thanksgiving holiday – about 2% more than last year – according to the major travel group AAA, which notes that the period is the single busiest holiday for travel in the US.

“Controllers have returned to their posts and normal operations can resume,” said Transportation Secretary Sean Duffy as he announced that the emergency order had been lifted. “Now we can refocus our efforts on surging controller hiring and building the brand new, state of the art air traffic control system the American people deserve.”

Air traffic controller absences were some of the most visible ramifications of the 43-day shutdown, the longest in US history. Many controllers said they were forced to take second jobs in order to make up for missing paycheques, and many of those who came to work said they experienced stress and exhaustion.

Airports scrambled to keep flights on time, sometimes relying on control towers miles away to guide planes in. The problem was made worse by an already existing shortage of controllers.

The emergency order had called for up to 10% of US domestic flights to be cut, and in the first week of November thousands of flights were cancelled and even more delayed.

According to the announcement ending the order, 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 no elaborate on which airlines allegedly did not cut flights, and how they might be penalised.

Across last Saturday and Sunday, there were only nine alerts put out by airports for grounded, scrapped or late flights due to staffing shortages – a stark contrast to the previous Saturday, 8 November, when those alerts reached a record high of 81, according to the transportation department.

With the end of the shutdown, controllers are set to receive back pay, and no longer face threats from Duffy of being fired for absences.