Roy Hodgson's side were due to meet up at the National Football Centre on Tuesday but have now been forced to alter their plans due to the bug.
The FA confirmed that Southgate's side have not suffered any symptoms of the virus but revealed that they would also change location as a precautionary measure.
"The FA has been advised of a suspected stomach virus that has been discovered on site at St George's Park and affected a small number of visitors over the weekend," read an FA statement. "To date, the England Under-21 squad has not experienced any symptoms related to the virus.
"They have been on site since Sunday. However, as a precautionary measure, the Under-21s are moving hotels and the England senior team will now not meet at St George's Park. Alternative accommodation and training arrangements have been made for both teams.
"This is an elite athlete precaution for the two senior teams. Normal operations continue for the SGP and hotel staff, customers and the public. To reiterate, these proactive steps have been taken by The FA as a precautionary measure."
It is believed that the virus was brought into the hotel from outside rather than it being a hygiene or cleanliness issue with the facilities.