Customers are only allowed to pick up online orders at 16 stores across the city and it's not clear how long the temporary measure would be in place, according to a report by Bloomberg.
"We regularly monitor conditions and we will adjust our health measures to support the well-being of customers and employees," Apple said in a statement on Monday.
New York City added 18,368 new COVID-19 cases on Monday with the 7-day average positive rate of COVID-19 testing hovering at 12.63 percent on Sunday, according to data issued by New York State on Monday.
Apple recently closed some stores in Florida, Georgia, New Hampshire, Texas and other places due to concerns over COVID-19 infections.
Apple required all of its customers in the United States to wear masks around two weeks ago.
In early 2020, Apple once closed all of its retail stores in the United States at the height of the COVID-19 pandemic and introduced protective measures after reopening.
Latest comments