The United boss revealed Rooney's illness was diagnosed by the club's own laboratory.
He also added that the squad had all taken malaria tablets ahead of the trip to Africa, while the club confirmed that the touring party have all had the required yellow fever vaccinations within the past 10 years.
Rooney's potential absence leaves Ferguson facing a selection dilemma ahead of the opening match of the season at home to Newcastle.
Cristiano Ronaldo will miss the first two months of the season following ankle surgery, winger Nani is suspended while midfielder Anderson is on Olympic duty with Brazil.
Rooney's problems could also reignite Ferguson's interest in signing Tottenham forward Dimitar Berbatov.
As it stands, Ferguson has only Carlos Tevez, untested youngster Fraizer Campbell and Louis Saha to choose from up front.
News conference: Sir Alex Ferguson
"I don't know whether we will have a team ready," said Ferguson. "Nani is suspended, Anderson is in the Olympic Games.
"(Michael) Carrick's come in this morning and he may play a part of the game on Sunday."
Rooney had sat on the sidelines when Manchester United played FA Cup winners Portsmouth in a friendly in Abuja on 27 July.
He then missed his club's two subsequent pre-season fixtures against Espanyol and Peterborough.
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