Soon after coronavirus began to spread, Sisi postponed moving the first civil servants to the new city and moved back the opening of a national museum adjoining the pyramids to next year.
Productivity dipped as companies adapted to health guidelines and some labourers stayed home.
But officials have sought to keep the mega-projects going to protect jobs, and after 10 days of slowdown construction had fully resumed at the new capital with a shift system, said Amr Khattab, spokesman for the Housing Ministry, which along with the military owns the company building the city.
"The proportion of the labour force that is present on site doesn't exceed 70%, so that the workers don't get too close," he said as he showed off the R5 neighbourhood, which includes about 24,000 housing units. "We work less intensively, but we do two shifts."
Sisi, who publicly quizzes officials responsible for infrastructure projects about timetables and costs, launched the new capital in 2015.
Designed as a high-tech smart city that will house 6.5 million people and relieve congestion in Cairo, it includes government and business districts, a giant park, and a diplomatic quarter as yet unbuilt.
One senior official said last year the cost of the whole project was about $58 billion. While some Egyptians see the new capital as a source of pride, others see it as extravagant and built to benefit a cocooned elite.
'RUNNING ON TIME'
"We have clear instructions from his excellency the president that the postponement of the opening is not a delay to the project," said Khattab. "The project is running on time."
Disinfection and other protective measures were visible at the construction site 45km (30 miles) east of the Nile, though some workers were only ordered to don masks when journalists started filming and others drove by crammed into a minibus. Egypt has confirmed more than 10,000 coronavirus cases, but none at the new capital.
Delays in payments to contractors and to imported supplies were additional risks, said Shams Eldin Youssef, a member of Egypt's union for construction contractors. Khattab said the government had contractors' payments in hand.
The Housing Ministry expects to deliver two residential districts by late 2021, while the business district should be finished by early 2022, said Ahmed al-Araby, deputy head of the new capital's development authority. Private developers and the army are building six other neighbourhoods.
In the government district, which Khattab said was 90% complete, ministry buildings fronted with vertical strips of white stone and darkened glass lead to an open area being planted with palm trees and mini obelisks in front of a domed parliament building.
To one side a large, low-rise presidential palace is under construction.
Sisi has urged people seeking work to head to new cities being built around the country, including the new capital, which Khattab said employs some 250,000 workers.
Critics have questioned the diversion of resources away from existing cities, including Cairo, parts of which are in slow decay.
"The question about how rational this is - whether it makes sense economically, whether it is doable, whether it's the best course of action - this question is not even asked," Ezzedine Fishere, an Egyptian writer and senior lecturer at Dartmouth College in the United States, said by phone.
On the other side of Cairo at the new museum next to the Giza pyramids, work has also been continuing at a slower pace.
In mid-April staffing levels sank to about 40%, with plans to recover gradually to 100%, said General Atef Muftah, who oversees the project.
(Writing by Aidan Lewis Editing by Ulf Laessing and Giles Elgood) ((Aidan.Lewis@tr.com; +20-1001174410;))