The 20-year-old was ruled out of Tuesday's win over Sweden with shingles, but Ferguson has insisted that the Football Association should have kept the information confidential.
"Phil Jones hopefully will be okay irrespective of Stuart Pearce declaring he had shingles, which we thought was doctor confidence," Ferguson said in a press conference.
"We're disappointed with that. There's not anything serious with the boy. He's got a mild condition but he should be okay, hopefully.
"What about doctor confidentiality? It is something we have to address, the FA is a big organisation, things can leak from a lot of different places. But that was a conversation between our doctor and theirs, and shouldn't have gone any further."
Meanwhile, Ferguson has revealed that winger Ashley Young has returned to fitness for this Sunday's Premier League clash against Everton.