The defender did not travel to Dortmund for Wednesday's friendly with Germany, instead going for scans and X-rays.
Jones, 25, was injured in an innocuous training ground tackle at St George's Park, with reports claiming it involved United team-mate Chris Smalling.
England manager Gareth Southgate did not reveal whether that was the case.
If the injury turns out to be a break and keeps Jones on the sidelines for a lengthy spell, it will cause a selection concern for United manager Jose Mourinho as they prepare for nine games in April.
Southgate said: "I don't know who it was with. It was just a nothing sort of thing really. It is very unfortunate for him and a huge disappointment as he has been playing very well and has had some injury difficulties in the past.
"We have respectfully sent him back to his club and we will know more once he has had scans and x-rays over the next 24-48 hours."
Southgate has no plans to call up a replacement as yet, but will "assess his options" after Wednesday's friendly in Germany, the FA said.
England play a World Cup qualifier at home to Lithuania on Sunday, for which Chelsea's Gary Cahill is suspended.
Southgate's other options at centre-back are Smalling, Manchester City's John Stones and Burnley's uncapped Michael Keane.
On Sunday, West Ham winger Michail Antonio withdrew from the England squad with a hamstring injury.
England squad:
Goalkeepers: Fraser Forster (Southampton), Joe Hart (Torino, on loan from Man City), Tom Heaton (Burnley).
Defenders: Ryan Bertrand (Southampton), Gary Cahill (Chelsea), Nathaniel Clyne (Liverpool), Michael Keane (Burnley), Luke Shaw (Man Utd), Chris Smalling (Man Utd), John Stones (Man City), Kyle Walker (Tottenham).
Midfielders: Dele Alli (Tottenham), Ross Barkley (Everton), Eric Dier (Tottenham), Adam Lallana (Liverpool), Jesse Lingard (Man Utd), Jake Livermore (West Brom), Alex Oxlade-Chamberlain (Arsenal), Nathan Redmond (Southampton), Raheem Sterling (Man City), James Ward-Prowse (Southampton).
Strikers: Jermain Defoe (Sunderland), Marcus Rashford (Man Utd), Jamie Vardy (Leicester).
Manchester United face an anxious wait to discover the seriousness of the toe injury that has forced Phil Jones out of the England squad.