United shut their Carrington training base on Monday after confirmation of positive coronavirus cases following PCR testing.
What was described as a small number of players and staff were sent home on Sunday after routine lateral flow tests came back positive. The club's academy, training in a separate bubble, was allowed to continue.
"The decision was taken following guidance from medical advisers due to the exceptional circumstances of an ongoing COVID-19 outbreak within Manchester United's squad," the league said in a statement.
"First team operations at the club's Carrington Training Complex were closed down today to help control the outbreak and minimise risk of further infection among players and staff."
United were due to travel to play Brentford in London on Tuesday night, with the match now to be rescheduled at a later date.
On Monday, a separate Premier League statement reported a record high in COVID positives across the league at 42 and said they are reverting to its emergency measures for all teams.
The statement read: "The safety of everybody is a priority and the Premier League is taking all precautionary steps in light of the recent rise in COVID-19 cases across the country. The League has reverted to its Emergency Measures, and will increase the frequency of both Lateral Flow and PCR COVID-19 testing of players and staff. The League can today confirm that between Monday 6 December and Sunday 12 December 3,805 players and club staff were tested for COVID-19. Of these, there were 42 new positive cases."